ENST00000644461.1:n.96+66012G>T

Variant names:

• chr15-38694167-G-T
• rs12912251
• ENST00000644461.1:n.96+66012G>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+66012G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,150 control chromosomes in the GnomAD database, including 5,079 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 0.25 (5079 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 24 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02694	ENST00000644461.1		n.96+66012G>T		intron	N/A
	LINC02694	ENST00000646232.1		n.163+4853G>T		intron	N/A
	LINC02694	ENST00000647456.1		n.572+4853G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37864 AN: 152032 Hom.: 5078 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.249 AC: 37885 AN: 152150 Hom.: 5079 Cov.: 32 AF XY: 0.247 AC XY: 18369 AN XY: 74370

African (AFR) AF: 0.172 AC: 7141 AN: 41506

American (AMR) AF: 0.265 AC: 4053 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3472

East Asian (EAS) AF: 0.0948 AC: 491 AN: 5178

South Asian (SAS) AF: 0.203 AC: 978 AN: 4820

European-Finnish (FIN) AF: 0.256 AC: 2706 AN: 10580

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20522 AN: 67982

Other (OTH) AF: 0.270 AC: 571 AN: 2116

Alfa AF: 0.287 Hom.: 18940

Bravo AF: 0.252

Asia WGS AF: 0.148 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs12912251; hg19: chr15-38986368;