13-113103654-G-A

Variant names:

• chr13-113103654-G-A
• rs3093230

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 0.195 in 152,100 control chromosomes in the GnomAD database, including 3,646 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 0.19 (3646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• 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: 0.195 AC: 29591 AN: 151982 Hom.: 3639 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.195 AC: 29600 AN: 152100 Hom.: 3646 Cov.: 32 AF XY: 0.200 AC XY: 14841 AN XY: 74346

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.174

Alfa AF: 0.206 Hom.: 599

Bravo AF: 0.190

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	-0.69
CADD	Benign	1.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093230; hg19: chr13-113757968; COSMIC: COSV60645537;