11-57237593-T-C

Variant names:

• chr11-57237593-T-C
• rs9943582

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 0.633 in 151,960 control chromosomes in the GnomAD database, including 30,845 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 0.63 (30845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.633 AC: 96139 AN: 151842 Hom.: 30797 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.633 AC: 96253 AN: 151960 Hom.: 30845 Cov.: 32 AF XY: 0.641 AC XY: 47591 AN XY: 74278

African (AFR) AF: 0.685 AC: 28363 AN: 41436

American (AMR) AF: 0.662 AC: 10132 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3470

East Asian (EAS) AF: 0.768 AC: 3947 AN: 5138

South Asian (SAS) AF: 0.721 AC: 3465 AN: 4806

European-Finnish (FIN) AF: 0.663 AC: 7012 AN: 10570

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38963 AN: 67926

Other (OTH) AF: 0.647 AC: 1368 AN: 2114

Alfa AF: 0.593 Hom.: 119471

Bravo AF: 0.632

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		0.20
PromoterAI		0.057	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9943582; hg19: chr11-57005067;