15-38663446-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02694	ENST00000643648.1		n.436+14966C>T		intron	N/A
	LINC02694	ENST00000644461.1		n.96+35291C>T		intron	N/A
	LINC02694	ENST00000646232.1		n.87-25792C>T		intron	N/A

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

African (AFR) AF: 0.951 AC: 38928 AN: 40940

American (AMR) AF: 0.781 AC: 11754 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3468

East Asian (EAS) AF: 0.951 AC: 4865 AN: 5118

South Asian (SAS) AF: 0.934 AC: 4460 AN: 4776

European-Finnish (FIN) AF: 0.781 AC: 7793 AN: 9984

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50478 AN: 67776

Other (OTH) AF: 0.805 AC: 1687 AN: 2096

Alfa AF: 0.789 Hom.: 15968

Bravo AF: 0.823

Asia WGS AF: 0.937 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4924281;

hg19: chr15-38955647;