chr13-98092309-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370328	XR_931670.4	n.73-25263G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293659	ENST00000717002.1	n.117-13146G>T		intron_variant	Intron 1 of 4
ENSG00000293659	ENST00000717003.1	n.91-13146G>T		intron_variant	Intron 1 of 4
ENSG00000293659	ENST00000717004.1	n.52-16499G>T		intron_variant	Intron 1 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs586851; hg19: chr13-98744563;