rs11926691

Variant names:

• chr3-82932937-C-A
• rs11926691

Your query was ambiguous. Multiple possible variants found:

• chr3-82932937-C-A
• chr3-82932937-C-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 0.507 in 151,676 control chromosomes in the GnomAD database, including 21,502 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 0.51 (21502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.507 AC: 76876 AN: 151558 Hom.: 21494 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.507 AC: 76901 AN: 151676 Hom.: 21502 Cov.: 32 AF XY: 0.512 AC XY: 37929 AN XY: 74128

African (AFR) AF: 0.253 AC: 10472 AN: 41418

American (AMR) AF: 0.611 AC: 9296 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2036 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4076 AN: 5136

South Asian (SAS) AF: 0.625 AC: 3014 AN: 4824

European-Finnish (FIN) AF: 0.604 AC: 6359 AN: 10524

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39818 AN: 67786

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.565 Hom.: 13733

Bravo AF: 0.494

Asia WGS AF: 0.699 AC: 2427 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.17
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11926691; hg19: chr3-82982088;