10-125446192-G-C

Variant names:

• chr10-125446192-G-C
• rs768761

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.676

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768761; hg19: chr10-127134761;