rs10189761

Variant names:

• chr2-646364-T-A
• rs10189761

Your query was ambiguous. Multiple possible variants found:

• chr2-646364-T-A
• chr2-646364-T-G

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 0.822 in 152,274 control chromosomes in the GnomAD database, including 51,566 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 0.82 (51566 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 125046 AN: 152156 Hom.: 51541 Cov.: 34

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.822 AC: 125128 AN: 152274 Hom.: 51566 Cov.: 34 AF XY: 0.825 AC XY: 61463 AN XY: 74456

African (AFR) AF: 0.782 AC: 32504 AN: 41546

American (AMR) AF: 0.859 AC: 13143 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3470

East Asian (EAS) AF: 0.918 AC: 4763 AN: 5186

South Asian (SAS) AF: 0.860 AC: 4147 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 9003 AN: 10608

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56315 AN: 68018

Other (OTH) AF: 0.826 AC: 1745 AN: 2112

Alfa AF: 0.823 Hom.: 6391

Bravo AF: 0.819

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.40
DANN	Benign	0.69
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs10189761; hg19: chr2-646364;