rs1316583

Variant names:

• chr15-38593845-C-T
• rs1316583
• ENST00000791581.1:n.274+13019C>T

Variant summary

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

The ENST00000791581.1(LINC02694):​n.274+13019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,198 control chromosomes in the GnomAD database, including 2,251 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 0.11 (2251 hom., cov: 32)
• Consequence: LINC02694 ENST00000791581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791581.1. 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
	LINC02694	ENST00000791581.1		n.274+13019C>T		intron	N/A
	LINC02694	ENST00000791584.1		n.269+13019C>T		intron	N/A
	LINC02694	ENST00000791586.1		n.95+13019C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17446 AN: 152080 Hom.: 2243 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.115 AC: 17496 AN: 152198 Hom.: 2251 Cov.: 32 AF XY: 0.115 AC XY: 8589 AN XY: 74416

African (AFR) AF: 0.304 AC: 12615 AN: 41486

American (AMR) AF: 0.130 AC: 1981 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1013 AN: 5188

South Asian (SAS) AF: 0.115 AC: 553 AN: 4826

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0125 AC: 853 AN: 68020

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0551 Hom.: 2471

Bravo AF: 0.132

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.67
DANN	Benign	0.78
PhyloP100		-0.31

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: rs1316583;

hg19: chr15-38886046;