13-36134863-T-C

Variant names:

• chr13-36134863-T-C
• rs9315390

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 0.777 in 152,164 control chromosomes in the GnomAD database, including 46,051 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 0.78 (46051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 2 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 = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118067 AN: 152046 Hom.: 45996 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.777 AC: 118182 AN: 152164 Hom.: 46051 Cov.: 32 AF XY: 0.779 AC XY: 57920 AN XY: 74384

African (AFR) AF: 0.799 AC: 33142 AN: 41496

American (AMR) AF: 0.771 AC: 11784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2633 AN: 3466

East Asian (EAS) AF: 0.919 AC: 4743 AN: 5162

South Asian (SAS) AF: 0.802 AC: 3869 AN: 4826

European-Finnish (FIN) AF: 0.757 AC: 8010 AN: 10584

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51366 AN: 68020

Other (OTH) AF: 0.769 AC: 1627 AN: 2116

Alfa AF: 0.761 Hom.: 5395

Bravo AF: 0.781

Asia WGS AF: 0.873 AC: 3035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9315390; hg19: chr13-36709000;