rs17574546

Variant names:

• chr15-38610275-A-C
• rs17574546
• ENST00000791582.1:n.150A>C

Variant summary

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

The ENST00000791582.1(LINC02694):​n.150A>C variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,076 control chromosomes in the GnomAD database, including 2,438 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 0.17 (2438 hom., cov: 32)
• Consequence: LINC02694 ENST00000791582.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 31 publications found

Genes affected

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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
LINC02694	ENST00000791582.1	n.150A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 5
LINC02694	ENST00000791585.1	n.115A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 4
LINC02694	ENST00000791592.1	n.122A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26105 AN: 151960 Hom.: 2439 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.172 AC: 26114 AN: 152076 Hom.: 2438 Cov.: 32 AF XY: 0.169 AC XY: 12528 AN XY: 74318

African (AFR) AF: 0.150 AC: 6205 AN: 41494

American (AMR) AF: 0.138 AC: 2115 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3470

East Asian (EAS) AF: 0.0451 AC: 233 AN: 5172

South Asian (SAS) AF: 0.0985 AC: 474 AN: 4814

European-Finnish (FIN) AF: 0.209 AC: 2202 AN: 10546

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13375 AN: 67990

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.185 Hom.: 11155

Bravo AF: 0.166

Asia WGS AF: 0.0680 AC: 238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.80
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs17574546; hg19: chr15-38902476;