ENST00000602579.1:n.257-1977G>T

Variant names:

• chr9-87012187-C-A
• ENST00000602579.1:n.257-1977G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000602579.1(LINC02893):​n.257-1977G>T variant causes a intron change. The variant allele was found at a frequency of 0.00000189 in 1,057,366 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: LINC02893 ENST00000602579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.61

Genes affected

LINC02893 (HGNC:55359): (long intergenic non-protein coding RNA 2893)

CDC20P1 (HGNC:29487): (cell division cycle 20 pseudogene 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC20P1		n.87012187C>A		intragenic_variant
LINC02893	NR_027471.1	n.257-1977G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02893	ENST00000602579.1	n.257-1977G>T		intron_variant	Intron 1 of 1	1
CDC20P1	ENST00000488829.1	n.536C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02893	ENST00000669870.1	n.550-1977G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000189 AC: 2 AN: 1057366 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 544170

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000269

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.82

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-89627102;