1-100385746-G-A

Position:

• chr1-100385746-G-A

Variant summary

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

The NM_003672.4(CDC14A):​c.217-4986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,082 control chromosomes in the GnomAD database, including 1,504 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 0.13 (1504 hom., cov: 32)
• Consequence: CDC14A NM_003672.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

CDC14A (HGNC:1718): (cell division cycle 14A) The protein encoded by this gene is a member of the dual specificity protein tyrosine phosphatase family. It is highly similar to Saccharomyces cerevisiae Cdc14, a protein tyrosine phosphatase involved in the exit of cell mitosis and initiation of DNA replication, suggesting a role in cell cycle control. This protein has been shown to interact with, and dephosphorylate tumor suppressor protein p53, and is thought to regulate the function of p53. Alternative splicing of this gene results in several transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC14A	NM_003672.4	c.217-4986G>A		intron_variant		ENST00000336454.5	NP_003663.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC14A	ENST00000336454.5	c.217-4986G>A		intron_variant		1	NM_003672.4	ENSP00000336739	A1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19841 AN: 151964 Hom.: 1505 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.130 AC: 19841 AN: 152082 Hom.: 1504 Cov.: 32 AF XY: 0.131 AC XY: 9717 AN XY: 74340

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.119

Alfa AF: 0.151 Hom.: 341

Bravo AF: 0.120

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.62

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: rs12096135; hg19: chr1-100851302;