rs976928

Variant names:

• chr11-81768001-A-G
• rs976928

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 0.453 in 151,890 control chromosomes in the GnomAD database, including 15,665 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 0.45 (15665 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.6 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: 0.453 AC: 68817 AN: 151772 Hom.: 15664 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.453 AC: 68837 AN: 151890 Hom.: 15665 Cov.: 31 AF XY: 0.455 AC XY: 33745 AN XY: 74224

African (AFR) AF: 0.418 AC: 17325 AN: 41414

American (AMR) AF: 0.414 AC: 6317 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1657 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2234 AN: 5136

South Asian (SAS) AF: 0.618 AC: 2979 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4536 AN: 10542

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32498 AN: 67920

Other (OTH) AF: 0.440 AC: 930 AN: 2116

Alfa AF: 0.476 Hom.: 9651

Bravo AF: 0.443

Asia WGS AF: 0.536 AC: 1862 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs976928; hg19: chr11-81479043; COSMIC: COSV53395901;