rs10511182

Variant names:

• chr3-101053991-C-G
• rs10511182

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 0.114 in 152,166 control chromosomes in the GnomAD database, including 1,103 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 0.11 (1103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 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: 0.114 AC: 17349 AN: 152048 Hom.: 1105 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.114 AC: 17343 AN: 152166 Hom.: 1103 Cov.: 32 AF XY: 0.111 AC XY: 8275 AN XY: 74380

African (AFR) AF: 0.0958 AC: 3978 AN: 41522

American (AMR) AF: 0.0975 AC: 1490 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0548 AC: 264 AN: 4816

European-Finnish (FIN) AF: 0.147 AC: 1556 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9392 AN: 67976

Other (OTH) AF: 0.111 AC: 234 AN: 2114

Alfa AF: 0.117 Hom.: 121

Bravo AF: 0.109

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.81
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10511182; hg19: chr3-100772835;