chr15-39104560-C-T

Variant names:

• chr15-39104560-C-T
• rs724729
• ENST00000558209.1:n.452-32952G>A

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.452-32952G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,122 control chromosomes in the GnomAD database, including 13,018 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 0.31 (13018 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259345	ENST00000558209.1	TSL:3	n.452-32952G>A		intron	N/A
	ENSG00000259345	ENST00000560197.6	TSL:5	n.64+14090G>A		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.68-32952G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46888 AN: 152004 Hom.: 12966 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.309 AC: 47004 AN: 152122 Hom.: 13018 Cov.: 32 AF XY: 0.300 AC XY: 22299 AN XY: 74368

African (AFR) AF: 0.752 AC: 31200 AN: 41480

American (AMR) AF: 0.161 AC: 2463 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.129 AC: 666 AN: 5176

South Asian (SAS) AF: 0.150 AC: 724 AN: 4818

European-Finnish (FIN) AF: 0.120 AC: 1266 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9501 AN: 67996

Other (OTH) AF: 0.263 AC: 557 AN: 2116

Alfa AF: 0.189 Hom.: 16851

Bravo AF: 0.333

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-0.057

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs724729;

hg19: chr15-39396761;