rs7633162

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-28485764-G-A
• chr3-28485764-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040432.4(ZCWPW2):​c.611-6363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,764 control chromosomes in the GnomAD database, including 13,157 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 0.41 (13157 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

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>A		intron	N/A	NP_001035522.1	Q504Y3
	ZCWPW2	NM_001324169.2		c.611-6363G>A		intron	N/A	NP_001311098.1	Q504Y3
	ZCWPW2	NM_001324170.2		c.493-6363G>A		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>A		intron	N/A	ENSP00000373278.2	Q504Y3
	ZCWPW2	ENST00000419130.5	TSL:1	c.263-6363G>A		intron	N/A	ENSP00000395687.1	H7C0L9
	ENSG00000283563	ENST00000635992.1	TSL:5	n.493-6363G>A		intron	N/A	ENSP00000489994.1	A0A1B0GU75

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62435 AN: 151646 Hom.: 13140 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.412 AC: 62490 AN: 151764 Hom.: 13157 Cov.: 32 AF XY: 0.412 AC XY: 30589 AN XY: 74158

African (AFR) AF: 0.354 AC: 14662 AN: 41360

American (AMR) AF: 0.445 AC: 6784 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3348 AN: 5164

South Asian (SAS) AF: 0.475 AC: 2291 AN: 4826

European-Finnish (FIN) AF: 0.386 AC: 4048 AN: 10492

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28609 AN: 67910

Other (OTH) AF: 0.438 AC: 920 AN: 2102

Alfa AF: 0.405 Hom.: 2472

Bravo AF: 0.412

Asia WGS AF: 0.552 AC: 1907 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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;