13-52943749-A-C

Variant names:

• chr13-52943749-A-C
• rs732949

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 0.0968 in 152,030 control chromosomes in the GnomAD database, including 1,039 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 0.097 (1039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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: 0.0968 AC: 14699 AN: 151914 Hom.: 1035 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0361

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0968 AC: 14723 AN: 152030 Hom.: 1039 Cov.: 32 AF XY: 0.104 AC XY: 7710 AN XY: 74296

African (AFR) AF: 0.0979 AC: 4060 AN: 41492

American (AMR) AF: 0.166 AC: 2528 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0361 AC: 125 AN: 3466

East Asian (EAS) AF: 0.291 AC: 1493 AN: 5132

South Asian (SAS) AF: 0.199 AC: 959 AN: 4816

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10558

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3901 AN: 67998

Other (OTH) AF: 0.0840 AC: 177 AN: 2108

Alfa AF: 0.0737 Hom.: 2809

Bravo AF: 0.0984

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.76
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs732949; hg19: chr13-53517884;