10-50938326-C-G

Variant names:

• chr10-50938326-C-G
• rs10761612

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 0.467 in 151,606 control chromosomes in the GnomAD database, including 18,401 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 0.47 (18401 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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: 0.467 AC: 70759 AN: 151496 Hom.: 18405 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.467 AC: 70760 AN: 151606 Hom.: 18401 Cov.: 31 AF XY: 0.470 AC XY: 34807 AN XY: 74036

African (AFR) AF: 0.218 AC: 9012 AN: 41296

American (AMR) AF: 0.502 AC: 7642 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3455 AN: 5144

South Asian (SAS) AF: 0.488 AC: 2344 AN: 4802

European-Finnish (FIN) AF: 0.582 AC: 6096 AN: 10476

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38646 AN: 67886

Other (OTH) AF: 0.482 AC: 1017 AN: 2110

Alfa AF: 0.387 Hom.: 1161

Bravo AF: 0.454

Asia WGS AF: 0.560 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	1.7
DANN	Benign	0.83
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs10761612; hg19: chr10-52698086;