rs493474

Positions:

• chr1-199391849-C-T

Variant summary

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

The NR_147896.1(LINC02789):​n.838C>T 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 0.323 in 151,946 control chromosomes in the GnomAD database, including 8,300 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 0.32 (8300 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: LINC02789 NR_147896.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LINC02789 (HGNC:54310): (long intergenic non-protein coding RNA 2789)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02789	NR_147896.1	n.838C>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02789	ENST00000452199.1	n.838C>T		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49027 AN: 151814 Hom.: 8307 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.380

GnomAD4 exome AF: 0.214 AC: 3 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.323 AC: 49014 AN: 151932 Hom.: 8300 Cov.: 32 AF XY: 0.318 AC XY: 23566 AN XY: 74222

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.375

Alfa AF: 0.357 Hom.: 4946

Bravo AF: 0.326

Asia WGS AF: 0.271 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs493474; hg19: chr1-199360977;