13-108163877-C-T

Variant names:

• chr13-108163877-C-T
• rs10492664

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.194

Alfa AF: 0.169 Hom.: 4901

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492664; hg19: chr13-108816225;