rs10501829

Variant names:

• chr11-95512390-G-A
• rs10501829

Your query was ambiguous. Multiple possible variants found:

• chr11-95512390-G-A
• chr11-95512390-G-T

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 0.147 in 152,166 control chromosomes in the GnomAD database, including 2,201 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 0.15 (2201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.146 AC: 22270 AN: 152048 Hom.: 2190 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.147 AC: 22315 AN: 152166 Hom.: 2201 Cov.: 32 AF XY: 0.148 AC XY: 11000 AN XY: 74412

African (AFR) AF: 0.272 AC: 11297 AN: 41482

American (AMR) AF: 0.0903 AC: 1380 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.172 AC: 891 AN: 5170

South Asian (SAS) AF: 0.164 AC: 792 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1391 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5642 AN: 68020

Other (OTH) AF: 0.119 AC: 250 AN: 2106

Alfa AF: 0.106 Hom.: 2162

Bravo AF: 0.148

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	17
DANN	Benign	0.57
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10501829; hg19: chr11-95245554;