rs2323397

Variant names:

• chr13-37188500-A-T
• rs2323397
• ENST00000827668.1:n.232+32776A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827668.1(ENSG00000307651):​n.232+32776A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 2 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827668.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307651	ENST00000827668.1		n.232+32776A>T		intron	N/A
	ENSG00000307674	ENST00000827784.1		n.385+1297A>T		intron	N/A
	ENSG00000307674	ENST00000827785.1		n.228+1297A>T		intron	N/A

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

African (AFR) AF: 0.238 AC: 9862 AN: 41494

American (AMR) AF: 0.107 AC: 1635 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3472

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5180

South Asian (SAS) AF: 0.0605 AC: 292 AN: 4826

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10610

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2536 AN: 67988

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2323397;

hg19: chr13-37762637;