rs7931462

Variant names:

• chr11-93051037-G-A
• rs7931462

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 0.0441 in 152,114 control chromosomes in the GnomAD database, including 256 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 0.044 (256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0441 AC: 6698 AN: 151996 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0441 AC: 6712 AN: 152114 Hom.: 256 Cov.: 32 AF XY: 0.0432 AC XY: 3212 AN XY: 74362

African (AFR) AF: 0.104 AC: 4308 AN: 41492

American (AMR) AF: 0.0248 AC: 379 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4812

European-Finnish (FIN) AF: 0.0165 AC: 174 AN: 10574

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0214 AC: 1458 AN: 67996

Other (OTH) AF: 0.0389 AC: 82 AN: 2110

Alfa AF: 0.0309 Hom.: 381

Bravo AF: 0.0468

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7931462; hg19: chr11-92784203;