18-56137762-T-A

Variant names:

• chr18-56137762-T-A
• rs1792745
• ENST00000590589.2:n.139T>A

Variant summary

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

The ENST00000590589.2(ENSG00000267732):​n.139T>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: ENSG00000267732 ENST00000590589.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 0 publications found

Genes affected

ENSG00000267732 (HGNC:):

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: 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=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590589.2. 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
	LINC03069	NR_148972.1		n.698+43587A>T		intron	N/A
	LINC01539	NR_040025.1		n.-226A>T		upstream_gene	N/A
	LINC01539	NR_040026.1		n.-226A>T		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267732	ENST00000590589.2	TSL:2	n.139T>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000267732	ENST00000654480.1		n.190T>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000267732	ENST00000659946.1		n.105T>A		non_coding_transcript_exon	Exon 1 of 4

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.077
DANN	Benign	0.31
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1792745; hg19: chr18-53804993;