rs7940866

Variant names:

• chr11-130947684-T-A
• rs7940866

Your query was ambiguous. Multiple possible variants found:

• chr11-130947684-T-A
• chr11-130947684-T-C

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 0.528 in 151,662 control chromosomes in the GnomAD database, including 21,537 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 0.53 (21537 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.528 AC: 80006 AN: 151546 Hom.: 21510 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.528 AC: 80089 AN: 151662 Hom.: 21537 Cov.: 31 AF XY: 0.527 AC XY: 39036 AN XY: 74086

African (AFR) AF: 0.623 AC: 25752 AN: 41320

American (AMR) AF: 0.477 AC: 7272 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2754 AN: 5120

South Asian (SAS) AF: 0.594 AC: 2837 AN: 4774

European-Finnish (FIN) AF: 0.483 AC: 5083 AN: 10524

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.489 AC: 33228 AN: 67904

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.495 Hom.: 2264

Bravo AF: 0.534

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7940866; hg19: chr11-130817579;