15-38606989-T-C

Variant names:

• chr15-38606989-T-C
• rs16967103
• ENST00000791581.1:n.275-5293T>C

Variant summary

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

The ENST00000791581.1(LINC02694):​n.275-5293T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,126 control chromosomes in the GnomAD database, including 3,831 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 0.21 (3831 hom., cov: 32)
• Consequence: LINC02694 ENST00000791581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 42 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791581.1. 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	ENST00000791581.1		n.275-5293T>C		intron	N/A
	LINC02694	ENST00000791584.1		n.270-5293T>C		intron	N/A
	LINC02694	ENST00000791586.1		n.96-5020T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32469 AN: 152008 Hom.: 3824 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.214 AC: 32497 AN: 152126 Hom.: 3831 Cov.: 32 AF XY: 0.209 AC XY: 15511 AN XY: 74360

African (AFR) AF: 0.296 AC: 12291 AN: 41476

American (AMR) AF: 0.152 AC: 2326 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3472

East Asian (EAS) AF: 0.0460 AC: 239 AN: 5194

South Asian (SAS) AF: 0.0990 AC: 476 AN: 4810

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13416 AN: 67996

Other (OTH) AF: 0.211 AC: 445 AN: 2110

Alfa AF: 0.202 Hom.: 4816

Bravo AF: 0.212

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.4
DANN	Benign	0.34
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs16967103; hg19: chr15-38899190;