chr3-167439281-C-T

Variant names:

• chr3-167439281-C-T
• rs10936538

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.375

Alfa AF: 0.258 Hom.: 605

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10936538; hg19: chr3-167157069;