rs10510935

Variant names:

• chr3-65230129-A-G
• rs10510935

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 0.135 in 152,196 control chromosomes in the GnomAD database, including 1,690 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 0.13 (1690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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: 0.135 AC: 20530 AN: 152078 Hom.: 1690 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.135 AC: 20540 AN: 152196 Hom.: 1690 Cov.: 32 AF XY: 0.137 AC XY: 10224 AN XY: 74410

African (AFR) AF: 0.0683 AC: 2836 AN: 41552

American (AMR) AF: 0.265 AC: 4046 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3464

East Asian (EAS) AF: 0.143 AC: 737 AN: 5164

South Asian (SAS) AF: 0.143 AC: 692 AN: 4830

European-Finnish (FIN) AF: 0.135 AC: 1436 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9943 AN: 67994

Other (OTH) AF: 0.127 AC: 267 AN: 2108

Alfa AF: 0.147 Hom.: 3121

Bravo AF: 0.144

Asia WGS AF: 0.137 AC: 475 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.082
DANN	Benign	0.30
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10510935; hg19: chr3-65215804;