chr15-38856448-T-C

Variant names:

• chr15-38856448-T-C
• rs2624265
• ENST00000644461.1:n.158+33389T>C

Variant summary

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

The ENST00000644461.1(LINC02694):​n.158+33389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,140 control chromosomes in the GnomAD database, including 7,338 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 0.28 (7338 hom., cov: 33)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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.158+33389T>C		intron_variant	Intron 2 of 4
LINC02694	ENST00000646232.1	n.225+33389T>C		intron_variant	Intron 3 of 3
LINC02694	ENST00000647456.1	n.658+123127T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42932 AN: 152022 Hom.: 7339 Cov.: 33

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.282 AC: 42934 AN: 152140 Hom.: 7338 Cov.: 33 AF XY: 0.283 AC XY: 21049 AN XY: 74368

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.304

Alfa AF: 0.361 Hom.: 23374

Bravo AF: 0.272

Asia WGS AF: 0.217 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2624265; hg19: chr15-39148649;