rs3093229

Positions:

• chr13-113103512-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 0.207 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.113103512C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.188

Alfa AF: 0.221 Hom.: 1030

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093229; hg19: chr13-113757826;