ENST00000765378.1:n.577C>A

Variant names:

• chr17-48643203-C-A
• rs2326017
• ENST00000765378.1:n.577C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000765378.1(LINC02086):​n.577C>A variant causes a non coding transcript exon 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: LINC02086 ENST00000765378.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 24 publications found

Genes affected

LINC02086 (HGNC:52936): (long intergenic non-protein coding RNA 2086)

LINC03057 (HGNC:56359): (long intergenic non-protein coding RNA 3057)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765378.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	NR_189645.1		n.577C>A		non_coding_transcript_exon	Exon 1 of 8
	LINC03057	NR_186590.1		n.248+3402G>T		intron	N/A
	LINC02086	NR_189644.1		n.452+125C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	ENST00000765378.1		n.577C>A		non_coding_transcript_exon	Exon 1 of 1
	LINC03057	ENST00000433510.3	TSL:2	n.446+3402G>T		intron	N/A
	LINC02086	ENST00000765377.1		n.270+125C>A		intron	N/A

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.: 28589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.020
DANN	Benign	0.71
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2326017; hg19: chr17-46720565;