rs2286812

Variant names:

• chr18-56050233-C-A
• rs2286812
• ENST00000382897.2:n.1067+5672G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-56050233-C-A
• chr18-56050233-C-G
• chr18-56050233-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000382897.2(LINC01539):​n.1067+5672G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LINC01539 ENST00000382897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 13 publications found

Genes affected

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01905	NR_146510.1	n.165+56C>A		intron_variant	Intron 2 of 3
LINC01905	NR_146511.1	n.165+56C>A		intron_variant	Intron 2 of 2
LINC03069	NR_148972.1	n.1067+5672G>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01539	ENST00000382897.2	n.1067+5672G>T		intron_variant	Intron 6 of 8	2
LINC01905	ENST00000585684.6	n.285+7889C>A		intron_variant	Intron 1 of 1	2
LINC01905	ENST00000589450.5	n.49+56C>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.74
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2286812; hg19: chr18-53717464;