rs1559033

Variant names:

• chr2-15744432-C-T
• rs1559033
• ENST00000436967.4:n.*93C>T

Variant summary

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

The ENST00000436967.4(LINC01804):​n.*93C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 285,326 control chromosomes in the GnomAD database, including 1,172 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 0.069 (1050 hom., cov: 32)
  • Exomes 𝑓: 0.016 (122 hom.)
• Consequence: LINC01804 ENST00000436967.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01804	ENST00000436967.4	n.*93C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10509 AN: 151998 Hom.: 1042 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00270

Gnomad FIN AF: 0.00774

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0588

GnomAD4 exome AF: 0.0159 AC: 2117 AN: 133210 Hom.: 122 AF XY: 0.0140 AC XY: 1036 AN XY: 73864

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.0210

Gnomad4 ASJ exome AF: 0.0366

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00250

Gnomad4 FIN exome AF: 0.00776

Gnomad4 NFE exome AF: 0.00780

Gnomad4 OTH exome AF: 0.0201

GnomAD4 genome AF: 0.0693 AC: 10548 AN: 152116 Hom.: 1050 Cov.: 32 AF XY: 0.0675 AC XY: 5019 AN XY: 74368

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00774

Gnomad4 NFE AF: 0.00899

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0423 Hom.: 65

Bravo AF: 0.0775

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559033; hg19: chr2-15884556;