chr3-13544961-A-G

Variant names:

• chr3-13544961-A-G
• rs6442396

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.763 AC: 31621 AN: 41468

American (AMR) AF: 0.840 AC: 12837 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5164 AN: 5168

South Asian (SAS) AF: 0.957 AC: 4622 AN: 4828

European-Finnish (FIN) AF: 0.891 AC: 9447 AN: 10598

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55973 AN: 68008

Other (OTH) AF: 0.805 AC: 1698 AN: 2110

Alfa AF: 0.830 Hom.: 37202

Bravo AF: 0.811

Asia WGS AF: 0.951 AC: 3301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.50
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6442396; hg19: chr3-13586461;