rs5015756
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001386010.1(ZCWPW1):c.754+141A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,144,758 control chromosomes in the GnomAD database, including 172,640 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 0.56 ( 24595 hom., cov: 32)
Exomes 𝑓: 0.54 ( 148045 hom. )
Consequence
ZCWPW1
NM_001386010.1 intron
NM_001386010.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.219
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZCWPW1 | NM_001386010.1 | c.754+141A>G | intron_variant | ENST00000684423.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZCWPW1 | ENST00000684423.1 | c.754+141A>G | intron_variant | NM_001386010.1 | P4 | ||||
ENST00000695704.1 | n.506-1499T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.561 AC: 85195AN: 151936Hom.: 24570 Cov.: 32
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GnomAD4 exome AF: 0.540 AC: 535858AN: 992704Hom.: 148045 AF XY: 0.544 AC XY: 271887AN XY: 499846
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GnomAD4 genome ? AF: 0.561 AC: 85265AN: 152054Hom.: 24595 Cov.: 32 AF XY: 0.557 AC XY: 41365AN XY: 74310
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at