rs12606608

chr18-56188320-C-T

Variant summary

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

The NR_148972.1(LINC03069):n.530G>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 0.522 in 151,980 control chromosomes in the GnomAD database, including 21,731 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 0.52 (21727 hom., cov: 31)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: LINC03069 NR_148972.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

Genes affected

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03069	NR_148972.1	n.530G>A		non_coding_transcript_exon_variant	2/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03069	ENST00000382897.2	n.530G>A		non_coding_transcript_exon_variant	2/9	2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79219 AN: 151840 Hom.: 21718 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.558

GnomAD4 exome AF: 0.500 AC: 11 AN: 22 Hom.: 4 Cov.: 0 AF XY: 0.438 AC XY: 7 AN XY: 16

Gnomad4 NFE exome AF: 0.556

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.522 AC: 79256 AN: 151958 Hom.: 21727 Cov.: 31 AF XY: 0.527 AC XY: 39120 AN XY: 74256

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.561

Alfa AF: 0.573 Hom.: 24367

Bravo AF: 0.512

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12606608; hg19: chr18-53855551;