rs13064954

chr3-157136953-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;