13-108163877-C-T

Variant names:

• chr13-108163877-C-T
• rs10492664

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 0.201 in 151,944 control chromosomes in the GnomAD database, including 3,303 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 0.20 (3303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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: 0.200 AC: 30441 AN: 151826 Hom.: 3285 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.201 AC: 30513 AN: 151944 Hom.: 3303 Cov.: 32 AF XY: 0.199 AC XY: 14794 AN XY: 74224

African (AFR) AF: 0.240 AC: 9938 AN: 41424

American (AMR) AF: 0.254 AC: 3874 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1635 AN: 5162

South Asian (SAS) AF: 0.163 AC: 788 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1703 AN: 10528

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11514 AN: 67976

Other (OTH) AF: 0.194 AC: 408 AN: 2102

Alfa AF: 0.176 Hom.: 10260

Bravo AF: 0.212

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10492664; hg19: chr13-108816225;