rs10501029

Variant names:

• chr11-25940552-A-G
• rs10501029

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 0.0642 in 152,268 control chromosomes in the GnomAD database, including 617 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 0.064 (617 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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: 0.0641 AC: 9760 AN: 152150 Hom.: 615 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.00962

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0642 AC: 9773 AN: 152268 Hom.: 617 Cov.: 33 AF XY: 0.0625 AC XY: 4655 AN XY: 74454

African (AFR) AF: 0.166 AC: 6892 AN: 41522

American (AMR) AF: 0.0369 AC: 564 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.0376 AC: 195 AN: 5188

South Asian (SAS) AF: 0.0513 AC: 248 AN: 4830

European-Finnish (FIN) AF: 0.00962 AC: 102 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0200 AC: 1359 AN: 68034

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.0507 Hom.: 70

Bravo AF: 0.0690

Asia WGS AF: 0.0420 AC: 145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.62
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10501029; hg19: chr11-25962099;