chr15-38711562-C-T

Variant names:

• chr15-38711562-C-T
• rs2643217
• ENST00000644461.1:n.96+83407C>T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+83407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,116 control chromosomes in the GnomAD database, including 2,355 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 (2355 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

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 = 0.216 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+83407C>T		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.52+8638C>T		intron_variant	Intron 1 of 2
LINC02694	ENST00000645994.1	n.142+14823C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23598 AN: 151998 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.155 AC: 23587 AN: 152116 Hom.: 2355 Cov.: 32 AF XY: 0.153 AC XY: 11384 AN XY: 74364

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.0550

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.188

Alfa AF: 0.168 Hom.: 420

Bravo AF: 0.150

Asia WGS AF: 0.0770 AC: 268 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	3.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2643217; hg19: chr15-39003763;