rs10763591

Positions:

• chr10-58945396-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;