5-55172296-A-T

Position:

• chr5-55172296-A-T

Variant summary

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

The NM_001170402.1(CDC20B):​c.126+292T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 325,882 control chromosomes in the GnomAD database, including 13,700 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 0.24 (5275 hom., cov: 32)
  • Exomes 𝑓: 0.30 (8425 hom.)
• Consequence: CDC20B NM_001170402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

CDC20B (HGNC:24222): (cell division cycle 20B) Predicted to enable anaphase-promoting complex binding activity and ubiquitin ligase activator activity. Predicted to be involved in anaphase-promoting complex-dependent catabolic process and positive regulation of anaphase-promoting complex-dependent catabolic process. Predicted to be part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]

MIR449C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC20B	NM_001170402.1	c.126+292T>A		intron_variant		ENST00000381375.7	NP_001163873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC20B	ENST00000381375.7	c.126+292T>A		intron_variant		1	NM_001170402.1	ENSP00000370781.2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36065 AN: 151964 Hom.: 5272 Cov.: 32

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.233

GnomAD3 exomes AF: 0.300 AC: 9047 AN: 30206 Hom.: 1498 AF XY: 0.306 AC XY: 4493 AN XY: 14672

Gnomad AFR exome AF: 0.0584

Gnomad AMR exome AF: 0.363

Gnomad ASJ exome AF: 0.229

Gnomad EAS exome AF: 0.367

Gnomad SAS exome AF: 0.260

Gnomad FIN exome AF: 0.219

Gnomad NFE exome AF: 0.328

Gnomad OTH exome AF: 0.307

GnomAD4 exome AF: 0.300 AC: 52172 AN: 173798 Hom.: 8425 Cov.: 0 AF XY: 0.296 AC XY: 27482 AN XY: 92836

Gnomad4 AFR exome AF: 0.0626

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.246

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.260

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.237 AC: 36078 AN: 152084 Hom.: 5275 Cov.: 32 AF XY: 0.233 AC XY: 17344 AN XY: 74316

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.236

Alfa AF: 0.274 Hom.: 762

Bravo AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.9
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs35770269; hg19: chr5-54468124; COSMIC: COSV57058374; COSMIC: COSV57058374;