ENST00000644461.1:n.96+78692G>A

Variant names:

• chr15-38706847-G-A
• rs903530
• ENST00000644461.1:n.96+78692G>A

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+78692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,150 control chromosomes in the GnomAD database, including 2,557 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 (2557 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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+78692G>A		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.52+3923G>A		intron_variant	Intron 1 of 2
LINC02694	ENST00000645994.1	n.142+10108G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25559 AN: 152032 Hom.: 2557 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.168 AC: 25551 AN: 152150 Hom.: 2557 Cov.: 32 AF XY: 0.168 AC XY: 12469 AN XY: 74368

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.195

Alfa AF: 0.211 Hom.: 4960

Bravo AF: 0.167

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903530; hg19: chr15-38999048;