13-36536762-A-C

Variant names:

• chr13-36536762-A-C
• rs4943389

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 0.588 in 151,720 control chromosomes in the GnomAD database, including 26,886 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 0.59 (26886 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89138 AN: 151602 Hom.: 26874 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.588 AC: 89196 AN: 151720 Hom.: 26886 Cov.: 31 AF XY: 0.593 AC XY: 43964 AN XY: 74156

African (AFR) AF: 0.528 AC: 21883 AN: 41428

American (AMR) AF: 0.648 AC: 9864 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1869 AN: 3462

East Asian (EAS) AF: 0.934 AC: 4823 AN: 5166

South Asian (SAS) AF: 0.706 AC: 3399 AN: 4812

European-Finnish (FIN) AF: 0.598 AC: 6313 AN: 10558

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39131 AN: 67776

Other (OTH) AF: 0.567 AC: 1194 AN: 2104

Alfa AF: 0.584 Hom.: 10168

Bravo AF: 0.589

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.52
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4943389; hg19: chr13-37110899;