3-138141265-C-T

Variant names:

• chr3-138141265-C-T
• rs397266

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 0.229 in 151,994 control chromosomes in the GnomAD database, including 4,684 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 (4684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.229 AC: 34813 AN: 151878 Hom.: 4683 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.229 AC: 34819 AN: 151994 Hom.: 4684 Cov.: 32 AF XY: 0.226 AC XY: 16772 AN XY: 74332

African (AFR) AF: 0.104 AC: 4306 AN: 41454

American (AMR) AF: 0.219 AC: 3352 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3468

East Asian (EAS) AF: 0.0532 AC: 275 AN: 5172

South Asian (SAS) AF: 0.195 AC: 938 AN: 4810

European-Finnish (FIN) AF: 0.281 AC: 2969 AN: 10552

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21045 AN: 67954

Other (OTH) AF: 0.247 AC: 521 AN: 2108

Alfa AF: 0.283 Hom.: 6848

Bravo AF: 0.218

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs397266; hg19: chr3-137860107;