chr1-74724768-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001889.4(CRYZ):c.54G>A(p.Gly18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 1,611,268 control chromosomes in the GnomAD database, including 460,803 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 0.77 ( 44757 hom., cov: 32)
Exomes 𝑓: 0.75 ( 416046 hom. )
Consequence
CRYZ
NM_001889.4 synonymous
NM_001889.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.223
Genes affected
CRYZ (HGNC:2419): (crystallin zeta) Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. The former class is also called phylogenetically-restricted crystallins. This gene encodes a taxon-specific crystallin protein which has NADPH-dependent quinone reductase activity distinct from other known quinone reductases. It lacks alcohol dehydrogenase activity although by similarity it is considered a member of the zinc-containing alcohol dehydrogenase family. Unlike other mammalian species, in humans, lens expression is low. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. One pseudogene is known to exist. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP7
?
Synonymous conserved (PhyloP=0.223 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYZ | NM_001889.4 | c.54G>A | p.Gly18= | synonymous_variant | 2/9 | ENST00000340866.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRYZ | ENST00000340866.10 | c.54G>A | p.Gly18= | synonymous_variant | 2/9 | 1 | NM_001889.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.766 AC: 116392AN: 151954Hom.: 44707 Cov.: 32
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GnomAD3 exomes AF: 0.755 AC: 188819AN: 250040Hom.: 71806 AF XY: 0.747 AC XY: 100895AN XY: 135122
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GnomAD4 exome AF: 0.754 AC: 1100107AN: 1459196Hom.: 416046 Cov.: 40 AF XY: 0.751 AC XY: 544994AN XY: 725906
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GnomAD4 genome ? AF: 0.766 AC: 116501AN: 152072Hom.: 44757 Cov.: 32 AF XY: 0.768 AC XY: 57045AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at