rs1241488

Variant names:

• chr14-25131926-T-C
• rs1241488
• ENST00000552425.2:n.150-4645A>G

Variant summary

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

The ENST00000552425.2(LINC02286):​n.150-4645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,036 control chromosomes in the GnomAD database, including 19,937 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 0.50 (19937 hom., cov: 32)
• Consequence: LINC02286 ENST00000552425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

Genes affected

LINC02286 (HGNC:53203): (long intergenic non-protein coding RNA 2286)

ENSG00000302997 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02286	NR_184204.1	n.279-4645A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02286	ENST00000552425.2	n.150-4645A>G		intron_variant	Intron 1 of 2	2
LINC02286	ENST00000665826.1	n.330-4645A>G		intron_variant	Intron 3 of 4
LINC02286	ENST00000668310.2	n.278-3638A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76601 AN: 151918 Hom.: 19929 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.504 AC: 76658 AN: 152036 Hom.: 19937 Cov.: 32 AF XY: 0.500 AC XY: 37150 AN XY: 74298

African (AFR) AF: 0.428 AC: 17775 AN: 41484

American (AMR) AF: 0.582 AC: 8882 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1979 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5176

South Asian (SAS) AF: 0.430 AC: 2069 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5294 AN: 10560

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37752 AN: 67952

Other (OTH) AF: 0.516 AC: 1090 AN: 2112

Alfa AF: 0.538 Hom.: 86779

Bravo AF: 0.506

Asia WGS AF: 0.339 AC: 1180 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	0.42
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1241488; hg19: chr14-25601132;