3-28485764-G-C

Variant names:

• chr3-28485764-G-C
• rs7633162
• NM_001040432.4:c.611-6363G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040432.4(ZCWPW2):​c.611-6363G>C variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZCWPW2 NM_001040432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 3 publications found

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]

ENSG00000283563 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040432.4. 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
	ZCWPW2	NM_001040432.4	MANE Select	c.611-6363G>C		intron	N/A	NP_001035522.1	Q504Y3
	ZCWPW2	NM_001324169.2		c.611-6363G>C		intron	N/A	NP_001311098.1	Q504Y3
	ZCWPW2	NM_001324170.2		c.493-6363G>C		intron	N/A	NP_001311099.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZCWPW2	ENST00000383768.7	TSL:1 MANE Select	c.611-6363G>C		intron	N/A	ENSP00000373278.2	Q504Y3
	ZCWPW2	ENST00000419130.5	TSL:1	c.263-6363G>C		intron	N/A	ENSP00000395687.1	H7C0L9
	ENSG00000283563	ENST00000635992.1	TSL:5	n.493-6363G>C		intron	N/A	ENSP00000489994.1	A0A1B0GU75

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.18

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

Other links and lift over

dbSNP: rs7633162; hg19: chr3-28527255;