3-13544961-A-G

Variant names:

• chr3-13544961-A-G
• rs6442396

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 0.822 in 152,142 control chromosomes in the GnomAD database, including 51,675 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 0.82 (51675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.822 AC: 124937 AN: 152024 Hom.: 51642 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.822 AC: 125026 AN: 152142 Hom.: 51675 Cov.: 32 AF XY: 0.828 AC XY: 61637 AN XY: 74396

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.805

Alfa AF: 0.829 Hom.: 25787

Bravo AF: 0.811

Asia WGS AF: 0.951 AC: 3301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6442396; hg19: chr3-13586461;