3-167439281-C-T

Variant names:

• chr3-167439281-C-T
• rs10936538

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 0.396 in 151,984 control chromosomes in the GnomAD database, including 12,326 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 0.40 (12326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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: 0.396 AC: 60116 AN: 151866 Hom.: 12314 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.396 AC: 60153 AN: 151984 Hom.: 12326 Cov.: 32 AF XY: 0.396 AC XY: 29384 AN XY: 74288

African (AFR) AF: 0.432 AC: 17918 AN: 41484

American (AMR) AF: 0.275 AC: 4205 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.127 AC: 652 AN: 5126

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4814

European-Finnish (FIN) AF: 0.498 AC: 5254 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28142 AN: 67958

Other (OTH) AF: 0.375 AC: 791 AN: 2110

Alfa AF: 0.268 Hom.: 681

Bravo AF: 0.376

Asia WGS AF: 0.244 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.14
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10936538; hg19: chr3-167157069;