13-98092309-C-A

Variant names:

• chr13-98092309-C-A
• rs586851
• ENST00000717002.1:n.117-13146G>T

Variant summary

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

The ENST00000717002.1(ENSG00000293659):​n.117-13146G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,026 control chromosomes in the GnomAD database, including 42,084 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 0.71 (42084 hom., cov: 32)
• Consequence: ENSG00000293659 ENST00000717002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 3 publications found

Genes affected

ENSG00000293659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717002.1. 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
	ENSG00000293659	ENST00000717002.1		n.117-13146G>T		intron	N/A
	ENSG00000293659	ENST00000717003.1		n.91-13146G>T		intron	N/A
	ENSG00000293659	ENST00000717004.1		n.52-16499G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107754 AN: 151908 Hom.: 42090 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.709 AC: 107777 AN: 152026 Hom.: 42084 Cov.: 32 AF XY: 0.701 AC XY: 52130 AN XY: 74318

African (AFR) AF: 0.455 AC: 18856 AN: 41402

American (AMR) AF: 0.632 AC: 9650 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3468

East Asian (EAS) AF: 0.125 AC: 645 AN: 5156

South Asian (SAS) AF: 0.588 AC: 2825 AN: 4804

European-Finnish (FIN) AF: 0.862 AC: 9123 AN: 10588

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.901 AC: 61295 AN: 68014

Other (OTH) AF: 0.720 AC: 1519 AN: 2110

Alfa AF: 0.826 Hom.: 166835

Bravo AF: 0.678

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.81
PhyloP100		-0.20

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: rs586851;

hg19: chr13-98744563;