rs1792745

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-56137762-T-A
• chr18-56137762-T-C
• chr18-56137762-T-G

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

ENSG00000267732 (HGNC:):

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

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

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=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372132	XR_007066384.1	n.169T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372132	XR_007066385.1	n.169T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372132	XR_007066386.1	n.23T>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267732	ENST00000590589.2	n.139T>A		non_coding_transcript_exon_variant	Exon 1 of 3	2
ENSG00000267732	ENST00000654480.1	n.190T>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000267732	ENST00000659946.1	n.105T>A		non_coding_transcript_exon_variant	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 v4.3

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

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-53804993;