13-36413132-T-C

Variant names:

• chr13-36413132-T-C
• rs4245377

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 0.55 in 152,062 control chromosomes in the GnomAD database, including 23,449 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 0.55 (23449 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• 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 = 0.857 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: 0.550 AC: 83583 AN: 151944 Hom.: 23438 Cov.: 33

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.550 AC: 83625 AN: 152062 Hom.: 23449 Cov.: 33 AF XY: 0.557 AC XY: 41377 AN XY: 74322

African (AFR) AF: 0.474 AC: 19683 AN: 41484

American (AMR) AF: 0.593 AC: 9048 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1730 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4552 AN: 5182

South Asian (SAS) AF: 0.711 AC: 3433 AN: 4826

European-Finnish (FIN) AF: 0.582 AC: 6150 AN: 10568

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37118 AN: 67954

Other (OTH) AF: 0.548 AC: 1154 AN: 2106

Alfa AF: 0.499 Hom.: 4604

Bravo AF: 0.548

Asia WGS AF: 0.759 AC: 2639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs4245377; hg19: chr13-36987269;