18-56188294-A-T

Variant names:

• chr18-56188294-A-T
• rs12604483
• ENST00000382897.2:n.556T>A

Variant summary

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

The ENST00000382897.2(LINC01539):​n.556T>A 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 0.453 in 152,082 control chromosomes in the GnomAD database, including 16,521 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 0.45 (16520 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LINC01539 ENST00000382897.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.15
• Publications: 13 publications found

Genes affected

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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03069	NR_148972.1	n.556T>A		non_coding_transcript_exon_variant	Exon 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01539	ENST00000382897.2	n.556T>A		non_coding_transcript_exon_variant	Exon 2 of 9	2
LINC01539	ENST00000715823.1	n.241T>A		non_coding_transcript_exon_variant	Exon 1 of 4
LINC01539	ENST00000765111.1	n.212T>A		non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68832 AN: 151956 Hom.: 16516 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.492

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.453 AC: 68862 AN: 152074 Hom.: 16520 Cov.: 32 AF XY: 0.459 AC XY: 34143 AN XY: 74326

African (AFR) AF: 0.306 AC: 12702 AN: 41502

American (AMR) AF: 0.501 AC: 7665 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3470

East Asian (EAS) AF: 0.838 AC: 4320 AN: 5154

South Asian (SAS) AF: 0.524 AC: 2526 AN: 4824

European-Finnish (FIN) AF: 0.529 AC: 5594 AN: 10566

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32977 AN: 67950

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.464 Hom.: 2318

Bravo AF: 0.446

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.073
DANN	Benign	0.32
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs12604483; hg19: chr18-53855525;