13-83372126-C-T

Variant names:

• chr13-83372126-C-T
• rs2105351

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 0.416 in 152,022 control chromosomes in the GnomAD database, including 16,634 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 0.42 (16634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 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: 0.417 AC: 63303 AN: 151904 Hom.: 16636 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.416 AC: 63299 AN: 152022 Hom.: 16634 Cov.: 32 AF XY: 0.412 AC XY: 30631 AN XY: 74298

African (AFR) AF: 0.103 AC: 4290 AN: 41512

American (AMR) AF: 0.554 AC: 8466 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1809 AN: 3472

East Asian (EAS) AF: 0.183 AC: 942 AN: 5148

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4849 AN: 10542

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39099 AN: 67942

Other (OTH) AF: 0.442 AC: 933 AN: 2112

Alfa AF: 0.340 Hom.: 1124

Bravo AF: 0.412

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2105351; hg19: chr13-83946261; COSMIC: COSV65545522;