rs41279402

Variant names:

• chr20-3805025-G-A
• rs41279402
• NM_021873.4:c.*64G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-3805025-G-A
• chr20-3805025-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_021873.4(CDC25B):​c.*64G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0055 in 1,544,086 control chromosomes in the GnomAD database, including 45 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 0.0034 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0057 (42 hom.)
• Consequence: CDC25B NM_021873.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 4 publications found

Genes affected

CDC25B (HGNC:1726): (cell division cycle 25B) CDC25B is a member of the CDC25 family of phosphatases. CDC25B activates the cyclin dependent kinase CDC2 by removing two phosphate groups and it is required for entry into mitosis. CDC25B shuttles between the nucleus and the cytoplasm due to nuclear localization and nuclear export signals. The protein is nuclear in the M and G1 phases of the cell cycle and moves to the cytoplasm during S and G2. CDC25B has oncogenic properties, although its role in tumor formation has not been determined. Multiple transcript variants for this gene exist. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021873.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC25B	NM_021873.4	MANE Select	c.*64G>A		3_prime_UTR	Exon 16 of 16	NP_068659.1	P30305-1
	CDC25B	NM_004358.5		c.*64G>A		3_prime_UTR	Exon 16 of 16	NP_004349.1	P30305-2
	CDC25B	NM_021872.4		c.*64G>A		3_prime_UTR	Exon 15 of 15	NP_068658.1	P30305-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC25B	ENST00000245960.10	TSL:1 MANE Select	c.*64G>A		3_prime_UTR	Exon 16 of 16	ENSP00000245960.5	P30305-1
	CDC25B	ENST00000439880.6	TSL:1	c.*64G>A		3_prime_UTR	Exon 16 of 16	ENSP00000405972.2	P30305-2
	CDC25B	ENST00000340833.4	TSL:1	c.*64G>A		3_prime_UTR	Exon 15 of 15	ENSP00000339170.4	P30305-3

Frequencies

GnomAD3 genomes AF: 0.00342 AC: 521 AN: 152174 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00113

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00616

Gnomad OTH AF: 0.00478

GnomAD4 exome AF: 0.00573 AC: 7977 AN: 1391794 Hom.: 42 Cov.: 26 AF XY: 0.00550 AC XY: 3790 AN XY: 689200

African (AFR) AF: 0.000817 AC: 26 AN: 31814

American (AMR) AF: 0.00306 AC: 118 AN: 38558

Ashkenazi Jewish (ASJ) AF: 0.0000423 AC: 1 AN: 23658

East Asian (EAS) AF: 0.00 AC: 0 AN: 38628

South Asian (SAS) AF: 0.00 AC: 0 AN: 80898

European-Finnish (FIN) AF: 0.000590 AC: 23 AN: 38960

Middle Eastern (MID) AF: 0.000221 AC: 1 AN: 4516

European-Non Finnish (NFE) AF: 0.00696 AC: 7502 AN: 1077124

Other (OTH) AF: 0.00531 AC: 306 AN: 57638

GnomAD4 genome AF: 0.00342 AC: 521 AN: 152292 Hom.: 3 Cov.: 33 AF XY: 0.00310 AC XY: 231 AN XY: 74448

African (AFR) AF: 0.00113 AC: 47 AN: 41564

American (AMR) AF: 0.00209 AC: 32 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00616 AC: 419 AN: 68018

Other (OTH) AF: 0.00473 AC: 10 AN: 2116

Alfa AF: 0.000639 Hom.: 0

Bravo AF: 0.00373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41279402;

hg19: chr20-3785672;