chr15-38663446-C-T

Variant names:

• chr15-38663446-C-T
• rs4924281
• ENST00000643648.1:n.436+14966C>T

Variant summary

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

The ENST00000643648.1(LINC02694):​n.436+14966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 150,412 control chromosomes in the GnomAD database, including 51,414 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 0.82 (51414 hom., cov: 25)
• Consequence: LINC02694 ENST00000643648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 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	ENST00000643648.1	n.436+14966C>T		intron_variant	Intron 4 of 4
LINC02694	ENST00000644461.1	n.96+35291C>T		intron_variant	Intron 1 of 4
LINC02694	ENST00000646232.1	n.87-25792C>T		intron_variant	Intron 1 of 3
LINC02694	ENST00000647456.1	n.152-25448C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.821 AC: 123435 AN: 150300 Hom.: 51349 Cov.: 25

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.821 AC: 123559 AN: 150412 Hom.: 51414 Cov.: 25 AF XY: 0.825 AC XY: 60461 AN XY: 73270

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.805

Alfa AF: 0.785 Hom.: 7997

Bravo AF: 0.823

Asia WGS AF: 0.937 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924281; hg19: chr15-38955647;