15-38713597-C-T

Variant names:

• chr15-38713597-C-T
• rs2643208
• ENST00000644461.1:n.96+85442C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644461.1(LINC02694):​n.96+85442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,992 control chromosomes in the GnomAD database, including 39,172 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 0.71 (39172 hom., cov: 31)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644461.1. 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	ENST00000644461.1		n.96+85442C>T		intron	N/A
	LINC02694	ENST00000645416.2		n.52+10673C>T		intron	N/A
	LINC02694	ENST00000645994.2		n.255+16858C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108372 AN: 151874 Hom.: 39126 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.714 AC: 108482 AN: 151992 Hom.: 39172 Cov.: 31 AF XY: 0.716 AC XY: 53183 AN XY: 74304

African (AFR) AF: 0.797 AC: 33024 AN: 41444

American (AMR) AF: 0.732 AC: 11178 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2467 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4654 AN: 5170

South Asian (SAS) AF: 0.740 AC: 3561 AN: 4812

European-Finnish (FIN) AF: 0.657 AC: 6929 AN: 10542

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44240 AN: 67968

Other (OTH) AF: 0.729 AC: 1541 AN: 2114

Alfa AF: 0.673 Hom.: 58632

Bravo AF: 0.722

Asia WGS AF: 0.824 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs2643208; hg19: chr15-39005798;