13-103408982-C-T

Variant names:

• chr13-103408982-C-T
• rs6491743

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 0.287 in 151,834 control chromosomes in the GnomAD database, including 13,350 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 0.29 (13350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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: 0.286 AC: 43462 AN: 151716 Hom.: 13290 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.0837

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0549

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.287 AC: 43587 AN: 151834 Hom.: 13350 Cov.: 32 AF XY: 0.280 AC XY: 20811 AN XY: 74244

African (AFR) AF: 0.772 AC: 31957 AN: 41406

American (AMR) AF: 0.224 AC: 3415 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0837 AC: 290 AN: 3464

East Asian (EAS) AF: 0.154 AC: 791 AN: 5152

South Asian (SAS) AF: 0.164 AC: 790 AN: 4812

European-Finnish (FIN) AF: 0.0549 AC: 580 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5159 AN: 67906

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.0464 Hom.: 48

Bravo AF: 0.321

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6491743; hg19: chr13-104061332;