18-56188294-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000382897.2(LINC03069):​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: LINC03069 ENST00000382897.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.15

Genes affected

LINC03069 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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
LINC03069	ENST00000382897.2	n.556T>A		non_coding_transcript_exon_variant	Exon 2 of 9	2

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

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.495

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12604483; hg19: chr18-53855525;