rs13272392

Variant names:

• chr8-23670998-T-A
• rs13272392
• ENST00000835200.1:n.475+2248T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23670998-T-A
• chr8-23670998-T-C
• chr8-23670998-T-G

Variant summary

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

The ENST00000835200.1(ENSG00000308589):​n.475+2248T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,048 control chromosomes in the GnomAD database, including 20,331 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 0.51 (20331 hom., cov: 32)
• Consequence: ENSG00000308589 ENST00000835200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 12 publications found

Genes affected

ENSG00000308589 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835200.1. 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
	ENSG00000308589	ENST00000835200.1		n.475+2248T>A		intron	N/A
	ENSG00000308589	ENST00000835201.1		n.1097+2248T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76794 AN: 151930 Hom.: 20328 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.505 AC: 76821 AN: 152048 Hom.: 20331 Cov.: 32 AF XY: 0.505 AC XY: 37496 AN XY: 74318

African (AFR) AF: 0.352 AC: 14612 AN: 41476

American (AMR) AF: 0.535 AC: 8162 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2030 AN: 3466

East Asian (EAS) AF: 0.706 AC: 3656 AN: 5178

South Asian (SAS) AF: 0.564 AC: 2719 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5205 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38683 AN: 67962

Other (OTH) AF: 0.509 AC: 1074 AN: 2112

Alfa AF: 0.524 Hom.: 2607

Bravo AF: 0.504

Asia WGS AF: 0.561 AC: 1944 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		1.6

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: rs13272392;

hg19: chr8-23528511;

COSMIC: COSV70618196;