10-125446192-G-C

Variant names:

• chr10-125446192-G-C
• rs768761

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 0.652 in 151,776 control chromosomes in the GnomAD database, including 33,229 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 0.65 (33229 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 0 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 = 0.845 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: 0.652 AC: 98946 AN: 151658 Hom.: 33215 Cov.: 30

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.652 AC: 98991 AN: 151776 Hom.: 33229 Cov.: 30 AF XY: 0.657 AC XY: 48676 AN XY: 74112

African (AFR) AF: 0.487 AC: 20155 AN: 41350

American (AMR) AF: 0.726 AC: 11083 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2544 AN: 3468

East Asian (EAS) AF: 0.866 AC: 4456 AN: 5144

South Asian (SAS) AF: 0.746 AC: 3586 AN: 4806

European-Finnish (FIN) AF: 0.691 AC: 7251 AN: 10488

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47666 AN: 67946

Other (OTH) AF: 0.676 AC: 1427 AN: 2110

Alfa AF: 0.592 Hom.: 1847

Bravo AF: 0.648

Asia WGS AF: 0.787 AC: 2736 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs768761; hg19: chr10-127134761;