13-49529275-T-A

Variant names:

• chr13-49529275-T-A
• rs3829366

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 0.476 in 151,990 control chromosomes in the GnomAD database, including 17,656 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 0.48 (17656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72279 AN: 151872 Hom.: 17645 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.476 AC: 72325 AN: 151990 Hom.: 17656 Cov.: 32 AF XY: 0.473 AC XY: 35112 AN XY: 74296

African (AFR) AF: 0.365 AC: 15123 AN: 41452

American (AMR) AF: 0.522 AC: 7972 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2423 AN: 5168

South Asian (SAS) AF: 0.320 AC: 1540 AN: 4810

European-Finnish (FIN) AF: 0.528 AC: 5557 AN: 10534

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36202 AN: 67958

Other (OTH) AF: 0.503 AC: 1060 AN: 2106

Alfa AF: 0.504 Hom.: 2407

Bravo AF: 0.476

Asia WGS AF: 0.389 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs3829366; hg19: chr13-50103411;