rs10943957

Variant names:

• chr6-83806805-T-A
• rs10943957

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 0.577 in 152,030 control chromosomes in the GnomAD database, including 31,203 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 0.58 (31203 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 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: 0.577 AC: 87661 AN: 151910 Hom.: 31204 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.577 AC: 87657 AN: 152030 Hom.: 31203 Cov.: 31 AF XY: 0.581 AC XY: 43160 AN XY: 74316

African (AFR) AF: 0.151 AC: 6281 AN: 41508

American (AMR) AF: 0.563 AC: 8592 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2556 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2584 AN: 5154

South Asian (SAS) AF: 0.710 AC: 3420 AN: 4816

European-Finnish (FIN) AF: 0.849 AC: 8951 AN: 10546

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53076 AN: 67964

Other (OTH) AF: 0.592 AC: 1247 AN: 2106

Alfa AF: 0.518 Hom.: 1678

Bravo AF: 0.536

Asia WGS AF: 0.609 AC: 2109 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.62
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10943957; hg19: chr6-84516524;