rs10958726

Variant names:

• chr8-42680766-G-T
• rs10958726

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 0.666 in 151,998 control chromosomes in the GnomAD database, including 35,912 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 0.67 (35912 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.666 AC: 101152 AN: 151880 Hom.: 35893 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.666 AC: 101204 AN: 151998 Hom.: 35912 Cov.: 31 AF XY: 0.670 AC XY: 49760 AN XY: 74298

African (AFR) AF: 0.401 AC: 16605 AN: 41444

American (AMR) AF: 0.727 AC: 11083 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2488 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4164 AN: 5158

South Asian (SAS) AF: 0.724 AC: 3488 AN: 4818

European-Finnish (FIN) AF: 0.759 AC: 8020 AN: 10562

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52947 AN: 67986

Other (OTH) AF: 0.690 AC: 1455 AN: 2108

Alfa AF: 0.716 Hom.: 14361

Bravo AF: 0.651

Asia WGS AF: 0.721 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10958726; hg19: chr8-42535909;