rs2869040

Variant names:

• chr15-78396492-C-T
• rs2869040
• ENST00000760515.1:n.229+5079C>T

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.229+5079C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,026 control chromosomes in the GnomAD database, including 33,564 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 0.66 (33564 hom., cov: 31)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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.229+5079C>T		intron_variant	Intron 2 of 2
ENSG00000299108	ENST00000760516.1	n.237+5079C>T		intron_variant	Intron 2 of 4
ENSG00000299108	ENST00000760517.1	n.*104C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99928 AN: 151908 Hom.: 33519 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.658 AC: 100031 AN: 152026 Hom.: 33564 Cov.: 31 AF XY: 0.660 AC XY: 49062 AN XY: 74286

African (AFR) AF: 0.800 AC: 33175 AN: 41478

American (AMR) AF: 0.652 AC: 9969 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3411 AN: 5134

South Asian (SAS) AF: 0.681 AC: 3283 AN: 4818

European-Finnish (FIN) AF: 0.629 AC: 6652 AN: 10574

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39230 AN: 67948

Other (OTH) AF: 0.654 AC: 1383 AN: 2116

Alfa AF: 0.592 Hom.: 50070

Bravo AF: 0.664

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2869040; hg19: chr15-78688834;