15-39148096-C-T

Position:

• chr15-39148096-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560484.1(ENSG00000259345):​n.68-76488G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 152,246 control chromosomes in the GnomAD database, including 102 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 0.025 (102 hom., cov: 32)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.518-76488G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.68-76488G>A		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1	n.159-24883C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3729 AN: 152128 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0245 AC: 3735 AN: 152246 Hom.: 102 Cov.: 32 AF XY: 0.0259 AC XY: 1928 AN XY: 74426

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.00207

Gnomad4 NFE AF: 0.00594

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0140 Hom.: 2

Bravo AF: 0.0254

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520120; hg19: chr15-39440297;