rs5015755

Positions:

• chr7-100415779-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386010.1(ZCWPW1):​c.754+196C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,114 control chromosomes in the GnomAD database, including 1,673 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 0.15 (1673 hom., cov: 30)
• Consequence: ZCWPW1 NM_001386010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

ZCWPW1 (HGNC:23486): (zinc finger CW-type and PWWP domain containing 1) Enables methyl-CpG binding activity and methylated histone binding activity. Predicted to be involved in meiosis I; positive regulation of DNA metabolic process; and spermatogenesis. Predicted to act upstream of or within homologous chromosome pairing at meiosis. Predicted to be located in XY body. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZCWPW1	NM_001386010.1	c.754+196C>A		intron_variant		ENST00000684423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZCWPW1	ENST00000684423.1	c.754+196C>A		intron_variant			NM_001386010.1	P4
	ENST00000695704.1	n.506-1554G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22246 AN: 151996 Hom.: 1675 Cov.: 30

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.146 AC: 22246 AN: 152114 Hom.: 1673 Cov.: 30 AF XY: 0.146 AC XY: 10835 AN XY: 74342

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.132

Alfa AF: 0.159 Hom.: 4096

Bravo AF: 0.140

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.59

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: rs5015755; hg19: chr7-100013402;