rs13317243

chr3-23143671-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;