3-28485764-G-A

Position:

• chr3-28485764-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZCWPW2	NM_001040432.4	c.611-6363G>A		intron_variant		ENST00000383768.7	NP_001035522.1
ZCWPW2	NM_001324169.2	c.611-6363G>A		intron_variant			NP_001311098.1
ZCWPW2	NM_001324170.2	c.493-6363G>A		intron_variant			NP_001311099.1
ZCWPW2	NR_136708.2	n.989-6363G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZCWPW2	ENST00000383768.7	c.611-6363G>A		intron_variant		1	NM_001040432.4	ENSP00000373278	P1
ZCWPW2	ENST00000419130.5	c.264-6363G>A		intron_variant		1		ENSP00000395687

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

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.438

Alfa AF: 0.406 Hom.: 2419

Bravo AF: 0.412

Asia WGS AF: 0.552 AC: 1907 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.35

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: rs7633162; hg19: chr3-28527255;