9-87012187-C-T

Position:

• chr9-87012187-C-T

Variant summary

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

The ENST00000488829.1(CDC20P1):​n.536C>T variant causes a non coding transcript exon 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: CDC20P1 ENST00000488829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.61

Genes affected

LINC02893 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CDC20P1		n.87012187C>T		intragenic_variant
LINC02893	NR_027471.1	n.257-1977G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02893	ENST00000602579.1	n.257-1977G>A		intron_variant		1
CDC20P1	ENST00000488829.1	n.536C>T		non_coding_transcript_exon_variant	1/1	6
LINC02893	ENST00000669870.1	n.550-1977G>A		intron_variant
LINC02893	ENST00000670732.1	n.258-1977G>A		intron_variant

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

Gnomad4 AFR exome AF: 0.00655

Gnomad4 AMR exome AF: 0.0659

Gnomad4 ASJ exome AF: 0.0367

Gnomad4 EAS exome AF: 0.000528

Gnomad4 SAS exome AF: 0.0593

Gnomad4 FIN exome AF: 0.0914

Gnomad4 NFE exome AF: 0.0490

Gnomad4 OTH exome AF: 0.0426

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

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0605

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0476 Hom.: 184

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12375908; hg19: chr9-89627102;