rs10511182

chr3-101053991-C-G

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 0.114 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0548

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.111

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511182; hg19: chr3-100772835;