ENST00000760515.1:n.76+13562G>A

Variant names:

• chr15-78375230-G-A
• rs2869036
• ENST00000760515.1:n.76+13562G>A

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.76+13562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,042 control chromosomes in the GnomAD database, including 50,343 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 0.81 (50343 hom., cov: 30)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 3 publications found

Genes affected

ENSG00000299108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299108	ENST00000760515.1	n.76+13562G>A		intron_variant	Intron 1 of 2
ENSG00000299108	ENST00000760516.1	n.-81G>A		upstream_gene_variant
ENSG00000299108	ENST00000760517.1	n.-96G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123179 AN: 151924 Hom.: 50275 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.811 AC: 123308 AN: 152042 Hom.: 50343 Cov.: 30 AF XY: 0.812 AC XY: 60323 AN XY: 74296

African (AFR) AF: 0.915 AC: 37973 AN: 41502

American (AMR) AF: 0.822 AC: 12562 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2900 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4127 AN: 5134

South Asian (SAS) AF: 0.776 AC: 3733 AN: 4808

European-Finnish (FIN) AF: 0.796 AC: 8421 AN: 10582

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.749 AC: 50918 AN: 67958

Other (OTH) AF: 0.804 AC: 1695 AN: 2108

Alfa AF: 0.774 Hom.: 23586

Bravo AF: 0.817

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.052
DANN	Benign	0.29
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2869036; hg19: chr15-78667572;