3-137466792-G-C

Variant names:

• chr3-137466792-G-C
• rs10935252

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 0.209 in 152,012 control chromosomes in the GnomAD database, including 3,542 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 0.21 (3542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.209 AC: 31725 AN: 151894 Hom.: 3543 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.209 AC: 31716 AN: 152012 Hom.: 3542 Cov.: 32 AF XY: 0.211 AC XY: 15651 AN XY: 74294

African (AFR) AF: 0.132 AC: 5479 AN: 41484

American (AMR) AF: 0.218 AC: 3327 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1681 AN: 5148

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2470 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16147 AN: 67946

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.213 Hom.: 435

Bravo AF: 0.203

Asia WGS AF: 0.289 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10935252; hg19: chr3-137185634;