chr15-38713697-C-T

Variant names:

• chr15-38713697-C-T
• rs4924292
• ENST00000644461.1:n.96+85542C>T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+85542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,998 control chromosomes in the GnomAD database, including 15,563 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 0.44 (15563 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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	ENST00000644461.1	n.96+85542C>T		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.52+10773C>T		intron_variant	Intron 1 of 2
LINC02694	ENST00000645994.2	n.255+16958C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67028 AN: 151880 Hom.: 15547 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.441 AC: 67101 AN: 151998 Hom.: 15563 Cov.: 32 AF XY: 0.442 AC XY: 32834 AN XY: 74286

African (AFR) AF: 0.548 AC: 22698 AN: 41438

American (AMR) AF: 0.439 AC: 6693 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3739 AN: 5180

South Asian (SAS) AF: 0.514 AC: 2476 AN: 4818

European-Finnish (FIN) AF: 0.333 AC: 3511 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25041 AN: 67988

Other (OTH) AF: 0.429 AC: 901 AN: 2100

Alfa AF: 0.451 Hom.: 6578

Bravo AF: 0.452

Asia WGS AF: 0.550 AC: 1910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.074
DANN	Benign	0.70
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs4924292; hg19: chr15-39005898;