rs1241488

chr14-25131926-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184204.1(LINC02286):n.279-4645A>G variant causes a intron, non coding transcript 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 NR_184204.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02286	NR_184204.1	n.279-4645A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02286	ENST00000665826.1	n.330-4645A>G		intron_variant, non_coding_transcript_variant
LINC02286	ENST00000552425.2	n.150-4645A>G		intron_variant, non_coding_transcript_variant		2
LINC02286	ENST00000668310.1	n.278-3638A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.516

Alfa AF: 0.546 Hom.: 41157

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1241488; hg19: chr14-25601132;