15-88603303-C-G

Variant names:

• chr15-88603303-C-G
• rs11637762
• ENST00000506090.5:n.343+94G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000506090.5(LINC01586):​n.343+94G>C 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: LINC01586 ENST00000506090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569

Genes affected

LINC01586 (HGNC:51434): (long intergenic non-protein coding RNA 1586)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01586	NR_120369.1	n.343+94G>C		intron_variant	Intron 2 of 2
LINC01586	NR_120370.1	n.333+94G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01586	ENST00000506090.5	n.343+94G>C		intron_variant	Intron 2 of 2	2
LINC01586	ENST00000560368.1	n.333+94G>C		intron_variant	Intron 2 of 2	3
LINC01586	ENST00000660022.1	n.119+94G>C		intron_variant	Intron 1 of 1
LINC01586	ENST00000558835.1	n.*80G>C		downstream_gene_variant		3

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11637762; hg19: chr15-89146534;