13-113103512-C-T

Variant names:

• chr13-113103512-C-T
• rs3093229

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 0.207 in 152,212 control chromosomes in the GnomAD database, including 3,829 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 0.21 (3829 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.207 AC: 31531 AN: 152094 Hom.: 3819 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.207 AC: 31560 AN: 152212 Hom.: 3829 Cov.: 33 AF XY: 0.212 AC XY: 15765 AN XY: 74414

African (AFR) AF: 0.107 AC: 4446 AN: 41560

American (AMR) AF: 0.256 AC: 3919 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2316 AN: 5168

South Asian (SAS) AF: 0.156 AC: 750 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3419 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15772 AN: 67996

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.217 Hom.: 1816

Bravo AF: 0.205

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
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: rs3093229; hg19: chr13-113757826;