3-174330139-C-G

Variant names:

• chr3-174330139-C-G
• rs5015152

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 0.871 in 151,788 control chromosomes in the GnomAD database, including 57,690 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 0.87 (57690 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.871 AC: 132061 AN: 151672 Hom.: 57655 Cov.: 28

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.871 AC: 132156 AN: 151788 Hom.: 57690 Cov.: 28 AF XY: 0.876 AC XY: 64938 AN XY: 74170

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.869

Alfa AF: 0.873 Hom.: 6768

Bravo AF: 0.869

Asia WGS AF: 0.926 AC: 3222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5015152; hg19: chr3-174047929;