rs10935268

Variant names:

• chr3-137728643-G-A
• rs10935268

Your query was ambiguous. Multiple possible variants found:

• chr3-137728643-G-A
• chr3-137728643-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.177 in 151,838 control chromosomes in the GnomAD database, including 3,095 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 0.18 (3095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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: 0.177 AC: 26901 AN: 151718 Hom.: 3084 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.177 AC: 26940 AN: 151838 Hom.: 3095 Cov.: 32 AF XY: 0.171 AC XY: 12703 AN XY: 74204

African (AFR) AF: 0.331 AC: 13701 AN: 41344

American (AMR) AF: 0.129 AC: 1961 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3466

East Asian (EAS) AF: 0.0611 AC: 316 AN: 5170

South Asian (SAS) AF: 0.0707 AC: 339 AN: 4794

European-Finnish (FIN) AF: 0.0726 AC: 766 AN: 10546

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8653 AN: 67948

Other (OTH) AF: 0.178 AC: 376 AN: 2108

Alfa AF: 0.142 Hom.: 8272

Bravo AF: 0.188

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	17
DANN	Benign	0.74
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10935268; hg19: chr3-137447485;