13-108163877-C-T

Position:

• chr13-108163877-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.108163877C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;