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

Variant names:

• chr9-87012187-C-T
• rs12375908
• ENST00000602579.1:n.257-1977G>A

Variant summary

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

The ENST00000602579.1(LINC02893):​n.257-1977G>A variant causes a intron change. The variant allele was found at a frequency of 0.0483 in 1,209,316 control chromosomes in the GnomAD database, including 1,762 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 0.042 (197 hom., cov: 32)
  • Exomes 𝑓: 0.049 (1565 hom.)
• Consequence: LINC02893 ENST00000602579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.61
• Publications: 1 publications found

Genes affected

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

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

GAS1RR (HGNC:52261): (GAS1 adjacent regulatory RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC20P1		n.87012187C>T		intragenic_variant
LINC02893	NR_027471.1	n.257-1977G>A		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>A		intron_variant	Intron 1 of 1	1
CDC20P1	ENST00000488829.1	n.536C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
GAS1RR	ENST00000846239.1	n.921C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6343 AN: 152198 Hom.: 197 Cov.: 32

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0425

GnomAD4 exome AF: 0.0492 AC: 52037 AN: 1057000 Hom.: 1565 Cov.: 16 AF XY: 0.0503 AC XY: 27361 AN XY: 543996

African (AFR) AF: 0.00655 AC: 169 AN: 25790

American (AMR) AF: 0.0659 AC: 2918 AN: 44246

Ashkenazi Jewish (ASJ) AF: 0.0367 AC: 866 AN: 23588

East Asian (EAS) AF: 0.000528 AC: 20 AN: 37886

South Asian (SAS) AF: 0.0593 AC: 4632 AN: 78110

European-Finnish (FIN) AF: 0.0914 AC: 4844 AN: 52972

Middle Eastern (MID) AF: 0.0358 AC: 178 AN: 4974

European-Non Finnish (NFE) AF: 0.0490 AC: 36410 AN: 742448

Other (OTH) AF: 0.0426 AC: 2000 AN: 46986

GnomAD4 genome AF: 0.0416 AC: 6343 AN: 152316 Hom.: 197 Cov.: 32 AF XY: 0.0442 AC XY: 3292 AN XY: 74470

African (AFR) AF: 0.0102 AC: 423 AN: 41586

American (AMR) AF: 0.0605 AC: 926 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0500 AC: 241 AN: 4820

European-Finnish (FIN) AF: 0.0869 AC: 922 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3569 AN: 68030

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.0464 Hom.: 219

Bravo AF: 0.0363

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		5.6

Splicing

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

Other links and lift over

dbSNP: rs12375908; hg19: chr9-89627102;