rs2323397

Variant names:

• chr13-37188500-A-T
• rs2323397

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 0.101 in 152,162 control chromosomes in the GnomAD database, including 1,370 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 0.10 (1370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.100 AC: 15243 AN: 152044 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.101 AC: 15294 AN: 152162 Hom.: 1370 Cov.: 32 AF XY: 0.0969 AC XY: 7211 AN XY: 74410

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.0126

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0728 Hom.: 100

Bravo AF: 0.116

Asia WGS AF: 0.0800 AC: 278 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2323397; hg19: chr13-37762637;