13-107131987-T-C

Variant names:

• chr13-107131987-T-C
• rs2806508

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 0.46 in 151,940 control chromosomes in the GnomAD database, including 16,539 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 0.46 (16539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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: 0.460 AC: 69860 AN: 151820 Hom.: 16541 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.460 AC: 69872 AN: 151940 Hom.: 16539 Cov.: 32 AF XY: 0.460 AC XY: 34162 AN XY: 74284

African (AFR) AF: 0.350 AC: 14481 AN: 41400

American (AMR) AF: 0.523 AC: 7984 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3035 AN: 5158

South Asian (SAS) AF: 0.384 AC: 1846 AN: 4810

European-Finnish (FIN) AF: 0.508 AC: 5367 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33980 AN: 67954

Other (OTH) AF: 0.474 AC: 1000 AN: 2108

Alfa AF: 0.484 Hom.: 30335

Bravo AF: 0.460

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2806508; hg19: chr13-107784335;