chr3-137113278-C-T

Variant names:

• chr3-137113278-C-T
• rs3796180

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 0.232 in 150,460 control chromosomes in the GnomAD database, including 4,339 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 0.23 (4339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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: 0.232 AC: 34893 AN: 150372 Hom.: 4322 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.232 AC: 34956 AN: 150460 Hom.: 4339 Cov.: 31 AF XY: 0.239 AC XY: 17502 AN XY: 73358

African (AFR) AF: 0.265 AC: 10880 AN: 41006

American (AMR) AF: 0.274 AC: 4143 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3464

East Asian (EAS) AF: 0.378 AC: 1936 AN: 5122

South Asian (SAS) AF: 0.245 AC: 1163 AN: 4756

European-Finnish (FIN) AF: 0.297 AC: 2959 AN: 9950

Middle Eastern (MID) AF: 0.173 AC: 49 AN: 284

European-Non Finnish (NFE) AF: 0.186 AC: 12618 AN: 67744

Other (OTH) AF: 0.222 AC: 461 AN: 2080

Alfa AF: 0.135 Hom.: 338

Bravo AF: 0.233

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.35
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3796180; hg19: chr3-136832120;