3-28413220-A-G

Position:

• chr3-28413220-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040432.4(ZCWPW2):​c.152A>G​(p.Lys51Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZCWPW2 NM_001040432.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.210

Genes affected

ZCWPW2 (HGNC:23574): (zinc finger CW-type and PWWP domain containing 2) Enables methylated histone binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05430174).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZCWPW2	NM_001040432.4	c.152A>G	p.Lys51Arg	missense_variant	3/10	ENST00000383768.7	NP_001035522.1
ZCWPW2	NM_001324169.2	c.152A>G	p.Lys51Arg	missense_variant	2/9		NP_001311098.1
ZCWPW2	NM_001324170.2	c.152A>G	p.Lys51Arg	missense_variant	2/7		NP_001311099.1
ZCWPW2	NR_136708.2	n.648A>G		non_coding_transcript_exon_variant	2/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZCWPW2	ENST00000383768.7	c.152A>G	p.Lys51Arg	missense_variant	3/10	1	NM_001040432.4	ENSP00000373278	P1
ZCWPW2	ENST00000428875.1	c.104A>G	p.Lys35Arg	missense_variant	1/4	5		ENSP00000393521
ZCWPW2	ENST00000420223.5	c.152A>G	p.Lys51Arg	missense_variant	5/6	5		ENSP00000395930

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 29, 2024

The c.152A>G (p.K51R) alteration is located in exon 2 (coding exon 1) of the ZCWPW2 gene. This alteration results from a A to G substitution at nucleotide position 152, causing the lysine (K) at amino acid position 51 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.3
DANN	Benign	0.96
DEOGEN2	Benign	0.0014	.;T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.92
FATHMM_MKL	Benign	0.027	N
LIST_S2	Benign	0.56	T;T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.054	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.29	.;N
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.31	N;N
REVEL	Benign	0.013
Sift	Benign	0.46	T;T
Sift4G	Benign	0.44	T;T
Polyphen		0.0030	.;B
Vest4		0.15
MutPred		0.33		Loss of ubiquitination at K51 (P = 0.0043);Loss of ubiquitination at K51 (P = 0.0043);
MVP		0.030
MPC		0.018
ClinPred		0.13	T
GERP RS		-1.9
Varity_R		0.13
gMVP		0.11

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-28454711;