ENST00000558382.2:n.276+12699T>C

Variant names:

• chr15-96367211-T-C
• rs8031676
• ENST00000558382.2:n.276+12699T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000558382.2(ENSG00000259275):​n.276+12699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,162 control chromosomes in the GnomAD database, including 19,583 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 0.50 (19583 hom., cov: 34)
• Consequence: ENSG00000259275 ENST00000558382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 4 publications found

Genes affected

ENSG00000259275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927263	XR_007064788.1	n.1281-5198T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259275	ENST00000558382.2	n.276+12699T>C		intron_variant	Intron 1 of 1	3
ENSG00000259275	ENST00000558499.2	n.123+12699T>C		intron_variant	Intron 1 of 1	4
ENSG00000259275	ENST00000650802.1	n.125-5198T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76278 AN: 152046 Hom.: 19575 Cov.: 34

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.502 AC: 76319 AN: 152162 Hom.: 19583 Cov.: 34 AF XY: 0.498 AC XY: 37058 AN XY: 74368

African (AFR) AF: 0.404 AC: 16773 AN: 41506

American (AMR) AF: 0.486 AC: 7425 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1885 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1585 AN: 5166

South Asian (SAS) AF: 0.431 AC: 2076 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6106 AN: 10580

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38694 AN: 68012

Other (OTH) AF: 0.496 AC: 1049 AN: 2114

Alfa AF: 0.543 Hom.: 101764

Bravo AF: 0.491

Asia WGS AF: 0.413 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs8031676; hg19: chr15-96910440;