rs13151462

Variant names:

• chr4-12669344-A-T
• rs13151462

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 0.488 in 151,904 control chromosomes in the GnomAD database, including 18,768 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 0.49 (18768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.488 AC: 74068 AN: 151786 Hom.: 18738 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.488 AC: 74139 AN: 151904 Hom.: 18768 Cov.: 32 AF XY: 0.494 AC XY: 36664 AN XY: 74232

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.446

Alfa AF: 0.447 Hom.: 1936

Bravo AF: 0.493

Asia WGS AF: 0.651 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13151462; hg19: chr4-12670968;