Genetic Variant formats, and the Human Genome Variation Society (HGVS) nomenclature of variants

[@adam7858]

Nice!! Very Informative Lecture with Good explanation of basic terminology of variant analysis

[@arushibatra7701]

Thank you! We are glad you found it helpful.

[@sudarshanwagh4004]

Thank you for the super-informative session!

[@GenomicsInIndia]

Glad it was helpful!

[@jayagandanj1772]

Precise and to the point!

[@GenomicsInIndia]

Thanks for your feedback

[@pranjalvats2372]

Very informative and well explained...👍

[@GenomicsInIndia]

Glad you liked it

[@divyadinesh7243]

Very well explained. Thank you for the session.

[@arushibatra7701]

Thank you! We are glad you found it helpful.

[@gurudeebanselvaraj8888]

Thanks, Ms.Batra...It is a great session, I feel a bit faster than the previous one. Could you please explain a bit more about the Variant Nomenclature slide, especially frameshift, in-frameshift, and intronic?

[@arushibatra7701]

Hello. Thank you for the feedback. I will try to be slower next time :)
Regd the question, a frameshift type of mutation occurs when the addition or deletion of DNA bases affects the reading frame of the gene. The reading frame consists of groups of 3 bases (called a codon), each codon coding for an amino acid. The frameshift mutation switches the grouping of these bases and changes the amino acid code. The resulting protein is typically non- functional. Frameshift mutations can all be insertions, deletions, and duplications. While, introns are noncoding sections of a gene and they are spliced out before the RNA molecule is translated into a protein. And in respect to HGVS nomenclature of these, variants within the intron are viewed in relation to their distance from the nearest exon. For more clarifications, please refer to the notes provided by us. And if any further doubts persists, please feel free to reach out to us!

[@gurudeebanselvaraj8888]

@@arushibatra7701 Thanks for your clarification. Now, I got your point. Sure, I will check the reference material and get back to you if any doubts.

[@gilsonborrgess6262]

Very good🎉
You explained very well, thanks

[@reemarosealappat6969]

Thank you
Nice presentation

[@nsankhyan]

Informative

[@bhavanasv]

Hello. Thank you for the lecture.

[@abdulkaderibrahim2393]

Thanks for the detailed lecture

[@arushibatra7701]

Thank you! We are glad you found it helpful.

[@xinformatics]

In the reference genome populations, what percentage of samples were taken from Indian people? Or the reference genome is based on US/Europe populations?

[@syednajeebashraf4101]

None from india or even Asian population !! Its mostly from US population .

[@aphroditechakraborty873]

Very informative session. Query: While mentioning amino acid changes for publications, is it necessary to use 3 alphabet notation, or can the 1 alphabet notation also be used?

[@arushibatra7701]

Hi thank you for the question. Acc to HGVS nomenclature, the three letter code is preferred over the single alphabet code. We can however use both to describe a variant.

[@aphroditechakraborty873]

@@arushibatra7701 Thank you.

[@arushibatra7701]

@@aphroditechakraborty873 Although I'm not sure about specifications regd. publications, but these are the general guidelines acc to HGVS Nomenclature.

[@BhavyaKansal18]

Had a small doubt at 50:10
Are the details mentioned in the example here not true? Because if it were 0/0 the alt and ref columns should have mentioned the same nucleotide.

[@arushibatra7701]

Hi.. Thank you for the question. Here it is just a dummy VCF that is used for demonstration. The various columns are not depicting any one single variant.

[@tanya72056]

Splendid stuff!

[@jassikagupta4431]

this session was great

[@arushibatra7701]

Thank you! We are glad you found it helpful.

[@mozahir1]

Thank you

[@srashtibisht624]

very informative lecture!

[@olubayokolawole4220]

You answer many question that re bothering me. Thank you.

[@AshishSingh-sy3gn]

Why are there multiple HGVS ids for the single variant in the clinvar database?

[@AshishSingh-sy3gn]

Why is there different positions for the same variant in the dbsnp, even when the genome assembly is same.

[@drmanishagupta1069]

nice lecture.

[@GenomicsInIndia]

Thanks and welcome

[@AshishSingh-sy3gn]

Why are we reporting 0|0 as a type of variant when in this case the base in both the allele is same as the reference at this position.

[@aishwaryasekar3815]

Aishwarya S. Good evening

[@sureshreddy8122]

Hello!

[@gauravkarve85]

Hi.

[@stxrl1ght34]

Hello

[@133ravi]

hi

[@Lunarbunny-c1x]

hello

[@mounikaendrakanti1639]

Hello

[@brijeshkumar-yx5on]

hello

[@AAK00419]

Hello

[@anamikasekhar5528]

Hello

[@dishamishra2973]

Hello