ENST00000500215.3:n.214+6224T>C

Variant names:

• chr14-77047501-T-C
• rs1986116
• ENST00000500215.3:n.214+6224T>C

Variant summary

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

The ENST00000500215.3(LINC02288):​n.214+6224T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,146 control chromosomes in the GnomAD database, including 40,898 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 0.73 (40898 hom., cov: 33)
• Consequence: LINC02288 ENST00000500215.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02288	NR_110554.1	n.229+6224T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02288	ENST00000500215.3	n.214+6224T>C		intron_variant	Intron 1 of 3	2
LINC02289	ENST00000716887.1	n.54-6255A>G		intron_variant	Intron 1 of 1
LINC02289	ENST00000716888.1	n.126+877A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111073 AN: 152026 Hom.: 40872 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.731 AC: 111149 AN: 152146 Hom.: 40898 Cov.: 33 AF XY: 0.735 AC XY: 54664 AN XY: 74390

African (AFR) AF: 0.634 AC: 26285 AN: 41458

American (AMR) AF: 0.832 AC: 12730 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3929 AN: 5166

South Asian (SAS) AF: 0.700 AC: 3379 AN: 4828

European-Finnish (FIN) AF: 0.772 AC: 8174 AN: 10586

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51366 AN: 68010

Other (OTH) AF: 0.749 AC: 1584 AN: 2116

Alfa AF: 0.744 Hom.: 28716

Bravo AF: 0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1986116; hg19: chr14-77513844;