chr7-50058101-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_007009.3(ZPBP):c.375T>C(p.Leu125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0365 in 1,613,794 control chromosomes in the GnomAD database, including 1,214 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.031 ( 89 hom., cov: 32)
Exomes 𝑓: 0.037 ( 1125 hom. )
Consequence
ZPBP
NM_007009.3 synonymous
NM_007009.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.268
Genes affected
ZPBP (HGNC:15662): (zona pellucida binding protein) ZPBP is one of several proteins that are thought to participate in secondary binding between acrosome-reacted sperm and the egg-specific extracellular matrix, the zona pellucida (McLeskey et al., 1998 [PubMed 9378618]).[supplied by OMIM, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 7-50058101-A-G is Benign according to our data. Variant chr7-50058101-A-G is described in ClinVar as [Benign]. Clinvar id is 3037675.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.268 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.031 (4727/152316) while in subpopulation NFE AF= 0.045 (3060/68028). AF 95% confidence interval is 0.0437. There are 89 homozygotes in gnomad4. There are 2212 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 89 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZPBP | NM_007009.3 | c.375T>C | p.Leu125= | synonymous_variant | 4/8 | ENST00000046087.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZPBP | ENST00000046087.7 | c.375T>C | p.Leu125= | synonymous_variant | 4/8 | 1 | NM_007009.3 | P4 | |
ZPBP | ENST00000419417.5 | c.372T>C | p.Leu124= | synonymous_variant | 4/8 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0311 AC: 4726AN: 152198Hom.: 89 Cov.: 32
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GnomAD3 exomes AF: 0.0311 AC: 7817AN: 251210Hom.: 163 AF XY: 0.0315 AC XY: 4278AN XY: 135768
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GnomAD4 exome AF: 0.0370 AC: 54116AN: 1461478Hom.: 1125 Cov.: 32 AF XY: 0.0368 AC XY: 26741AN XY: 727044
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GnomAD4 genome ? AF: 0.0310 AC: 4727AN: 152316Hom.: 89 Cov.: 32 AF XY: 0.0297 AC XY: 2212AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ZPBP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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