chr18-56137762-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000590589.2(ENSG00000267732):​n.139T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,174 control chromosomes in the GnomAD database, including 54,114 homozygotes. 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: 𝑓 0.84 (54114 hom., cov: 32)
• Consequence: ENSG00000267732 ENST00000590589.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

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>G		intron	N/A
	LINC01539	NR_040025.1		n.-226A>G		upstream_gene	N/A
	LINC01539	NR_040026.1		n.-226A>G		upstream_gene	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127160 AN: 152056 Hom.: 54070 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.836 AC: 127254 AN: 152174 Hom.: 54114 Cov.: 32 AF XY: 0.828 AC XY: 61615 AN XY: 74394

African (AFR) AF: 0.904 AC: 37509 AN: 41508

American (AMR) AF: 0.695 AC: 10623 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2988 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2005 AN: 5160

South Asian (SAS) AF: 0.701 AC: 3378 AN: 4822

European-Finnish (FIN) AF: 0.851 AC: 9027 AN: 10604

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58923 AN: 68020

Other (OTH) AF: 0.833 AC: 1758 AN: 2110

Alfa AF: 0.850 Hom.: 92125

Bravo AF: 0.824

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.40
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;