20-3657463-A-G

Variant names:

• chr20-3657463-A-G
• rs692862

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 0.838 in 152,144 control chromosomes in the GnomAD database, including 53,718 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 0.84 (53718 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.88 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: 0.838 AC: 127441 AN: 152026 Hom.: 53680 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.838 AC: 127536 AN: 152144 Hom.: 53718 Cov.: 31 AF XY: 0.836 AC XY: 62160 AN XY: 74384

African (AFR) AF: 0.761 AC: 31541 AN: 41472

American (AMR) AF: 0.893 AC: 13652 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4006 AN: 5146

South Asian (SAS) AF: 0.882 AC: 4251 AN: 4818

European-Finnish (FIN) AF: 0.796 AC: 8447 AN: 10606

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59923 AN: 68020

Other (OTH) AF: 0.852 AC: 1802 AN: 2114

Alfa AF: 0.851 Hom.: 17676

Bravo AF: 0.841

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.33
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs692862; hg19: chr20-3638110;