rs11761231

Variant names:

• chr7-131685280-T-C
• rs11761231

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 0.654 in 152,108 control chromosomes in the GnomAD database, including 33,614 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 0.65 (33614 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99464 AN: 151990 Hom.: 33585 Cov.: 33

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.654 AC: 99540 AN: 152108 Hom.: 33614 Cov.: 33 AF XY: 0.648 AC XY: 48181 AN XY: 74340

African (AFR) AF: 0.766 AC: 31817 AN: 41520

American (AMR) AF: 0.540 AC: 8246 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5168

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4820

European-Finnish (FIN) AF: 0.620 AC: 6549 AN: 10562

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44426 AN: 67984

Other (OTH) AF: 0.663 AC: 1399 AN: 2110

Alfa AF: 0.644 Hom.: 136331

Bravo AF: 0.654

Asia WGS AF: 0.413 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11761231; hg19: chr7-131370039;