rs595113

Variant names:

• chr1-199390312-C-A
• rs595113
• ENST00000452199.1:n.310-1009C>A

Variant summary

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

The ENST00000452199.1(LINC02789):​n.310-1009C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,874 control chromosomes in the GnomAD database, including 8,456 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 0.33 (8456 hom., cov: 32)
• Consequence: LINC02789 ENST00000452199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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 rank	MANE	Protein	UniProt
LINC02789	NR_147896.1	n.310-1009C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02789	ENST00000452199.1	n.310-1009C>A		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49640 AN: 151756 Hom.: 8463 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.361

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

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.327 AC: 49626 AN: 151874 Hom.: 8456 Cov.: 32 AF XY: 0.321 AC XY: 23850 AN XY: 74192

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.360

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: 0.376

Alfa AF: 0.325 Hom.: 1068

Bravo AF: 0.331

Asia WGS AF: 0.269 AC: 938 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs595113; hg19: chr1-199359440;