2-19791974-T-G

Variant names:

• chr2-19791974-T-G
• rs4666349

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.919 in 152,296 control chromosomes in the GnomAD database, including 64,500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64500 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139829 AN: 152178 Hom.: 64434 Cov.: 34

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.913

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.919 AC: 139954 AN: 152296 Hom.: 64500 Cov.: 34 AF XY: 0.922 AC XY: 68634 AN XY: 74464

African (AFR) AF: 0.980 AC: 40724 AN: 41574

American (AMR) AF: 0.933 AC: 14284 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3284 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5178

South Asian (SAS) AF: 0.980 AC: 4730 AN: 4828

European-Finnish (FIN) AF: 0.877 AC: 9301 AN: 10606

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59419 AN: 68016

Other (OTH) AF: 0.915 AC: 1934 AN: 2114

Alfa AF: 0.902 Hom.: 32977

Bravo AF: 0.924

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	10
DANN	Benign	0.42
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4666349; hg19: chr2-19991735;