rs10763591

Variant names:

• chr10-58945396-G-A
• rs10763591

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 0.139 in 151,896 control chromosomes in the GnomAD database, including 1,591 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 0.14 (1591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 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: 0.139 AC: 21036 AN: 151780 Hom.: 1588 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.139 AC: 21058 AN: 151896 Hom.: 1591 Cov.: 32 AF XY: 0.138 AC XY: 10230 AN XY: 74188

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.0362

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.133

Alfa AF: 0.141 Hom.: 288

Bravo AF: 0.136

Asia WGS AF: 0.0790 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10763591; hg19: chr10-60705156;