15-38867389-C-T

Variant names:

• chr15-38867389-C-T
• rs2725795
• ENST00000560197.6:n.977+581G>A

Variant summary

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

The ENST00000560197.6(ENSG00000259345):​n.977+581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,986 control chromosomes in the GnomAD database, including 32,848 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 0.65 (32848 hom., cov: 31)
• Consequence: ENSG00000259345 ENST00000560197.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 5 publications found

Genes affected

ENSG00000259345 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_001751487.2	n.287+581G>A		intron_variant	Intron 2 of 2
LOC105370777	XR_932130.3	n.244+581G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.6	n.977+581G>A		intron_variant	Intron 7 of 7	5
LINC02694	ENST00000644461.1	n.158+44330C>T		intron_variant	Intron 2 of 4
LINC02694	ENST00000646232.1	n.225+44330C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97993 AN: 151868 Hom.: 32796 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.646 AC: 98108 AN: 151986 Hom.: 32848 Cov.: 31 AF XY: 0.645 AC XY: 47924 AN XY: 74264

African (AFR) AF: 0.783 AC: 32455 AN: 41468

American (AMR) AF: 0.713 AC: 10876 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2073 AN: 3466

East Asian (EAS) AF: 0.921 AC: 4756 AN: 5164

South Asian (SAS) AF: 0.667 AC: 3221 AN: 4826

European-Finnish (FIN) AF: 0.478 AC: 5034 AN: 10526

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.557 AC: 37834 AN: 67960

Other (OTH) AF: 0.650 AC: 1374 AN: 2114

Alfa AF: 0.590 Hom.: 46731

Bravo AF: 0.672

Asia WGS AF: 0.821 AC: 2854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2725795; hg19: chr15-39159590;