rs493474

Variant names:

• chr1-199391849-C-T
• rs493474
• ENST00000452199.1:n.838C>T

Variant summary

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

The ENST00000452199.1(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 ENST00000452199.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02789	NR_147896.1	n.838C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02789	ENST00000452199.1	n.838C>T		non_coding_transcript_exon_variant	Exon 4 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.256 AC: 10606 AN: 41452

American (AMR) AF: 0.358 AC: 5454 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.176 AC: 905 AN: 5148

South Asian (SAS) AF: 0.419 AC: 2013 AN: 4804

European-Finnish (FIN) AF: 0.220 AC: 2327 AN: 10574

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24667 AN: 67934

Other (OTH) AF: 0.375 AC: 792 AN: 2110

Alfa AF: 0.357 Hom.: 5514

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs493474; hg19: chr1-199360977;