3-137283682-G-C

Variant names:

• chr3-137283682-G-C
• rs9853631

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 0.343 in 151,668 control chromosomes in the GnomAD database, including 11,082 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 0.34 (11082 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.32
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 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: 0.343 AC: 52046 AN: 151550 Hom.: 11076 Cov.: 30

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.343 AC: 52053 AN: 151668 Hom.: 11082 Cov.: 30 AF XY: 0.339 AC XY: 25153 AN XY: 74098

African (AFR) AF: 0.0938 AC: 3888 AN: 41436

American (AMR) AF: 0.436 AC: 6624 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1711 AN: 3462

East Asian (EAS) AF: 0.343 AC: 1764 AN: 5142

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3800 AN: 10494

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31722 AN: 67828

Other (OTH) AF: 0.404 AC: 847 AN: 2094

Alfa AF: 0.375 Hom.: 1472

Bravo AF: 0.339

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Benign	0.74
PhyloP100		6.3

Splicing

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

Other links and lift over

dbSNP: rs9853631; hg19: chr3-137002524;