chr15-38699255-G-A

Position:

• chr15-38699255-G-A

Variant summary

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

The NR_160786.1(LINC02694):​n.1260G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,124 control chromosomes in the GnomAD database, including 2,455 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 0.16 (2455 hom., cov: 32)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: LINC02694 NR_160786.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02694	NR_160786.1	n.1260G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02694	ENST00000644461.1	n.96+71100G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24874 AN: 151974 Hom.: 2455 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.188 AC: 6 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.179

GnomAD4 genome AF: 0.163 AC: 24863 AN: 152092 Hom.: 2455 Cov.: 32 AF XY: 0.163 AC XY: 12119 AN XY: 74356

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0952

Gnomad4 SAS AF: 0.0581

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.189

Alfa AF: 0.204 Hom.: 5645

Bravo AF: 0.161

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1495186; hg19: chr15-38991456;