rs13064954

Variant names:

• chr3-157136953-G-A
• rs13064954

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 0.0784 in 152,206 control chromosomes in the GnomAD database, including 614 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 0.078 (614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 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: 0.0784 AC: 11917 AN: 152088 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0784 AC: 11933 AN: 152206 Hom.: 614 Cov.: 32 AF XY: 0.0798 AC XY: 5940 AN XY: 74420

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.0763

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0466 Hom.: 354

Bravo AF: 0.0836

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13064954; hg19: chr3-156854742;