ENST00000500215.3:n.215-7579G>A

Variant names:

• chr14-77051959-G-A
• rs17105232
• ENST00000500215.3:n.215-7579G>A

Variant summary

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

The ENST00000500215.3(LINC02288):​n.215-7579G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,832 control chromosomes in the GnomAD database, including 3,176 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 0.19 (3176 hom., cov: 30)
• Consequence: LINC02288 ENST00000500215.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 7 publications found

Genes affected

LINC02288 (HGNC:27505): (long intergenic non-protein coding RNA 2288)

LINC02289 (HGNC:53205): (long intergenic non-protein coding RNA 2289)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02288	NR_110554.1	n.230-7579G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02288	ENST00000500215.3	n.215-7579G>A		intron_variant	Intron 1 of 3	2
LINC02289	ENST00000554043.2	n.231-3538C>T		intron_variant	Intron 2 of 2	2
LINC02289	ENST00000716887.1	n.54-10713C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28865 AN: 151714 Hom.: 3181 Cov.: 30

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.190 AC: 28849 AN: 151832 Hom.: 3176 Cov.: 30 AF XY: 0.190 AC XY: 14067 AN XY: 74194

African (AFR) AF: 0.0729 AC: 3021 AN: 41452

American (AMR) AF: 0.165 AC: 2514 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3464

East Asian (EAS) AF: 0.288 AC: 1482 AN: 5142

South Asian (SAS) AF: 0.198 AC: 948 AN: 4792

European-Finnish (FIN) AF: 0.232 AC: 2440 AN: 10518

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16781 AN: 67902

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.227 Hom.: 17671

Bravo AF: 0.181

Asia WGS AF: 0.245 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		0.053
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17105232; hg19: chr14-77518302;