rs2323397

Positions:

• chr13-37188500-A-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 0.101 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.37188500A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;