rs13317243

Variant names:

• chr3-23143671-G-C
• rs13317243

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 0.147 in 152,128 control chromosomes in the GnomAD database, including 2,078 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 0.15 (2078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 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: 0.147 AC: 22419 AN: 152010 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.147 AC: 22431 AN: 152128 Hom.: 2078 Cov.: 32 AF XY: 0.147 AC XY: 10941 AN XY: 74356

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.159

Alfa AF: 0.173 Hom.: 340

Bravo AF: 0.145

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13317243; hg19: chr3-23185162;