rs10838527
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021117.5(CRY2):c.*732A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,214 control chromosomes in the GnomAD database, including 1,504 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 0.12 ( 1504 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CRY2
NM_021117.5 3_prime_UTR
NM_021117.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.512
Genes affected
CRY2 (HGNC:2385): (cryptochrome circadian regulator 2) This gene encodes a flavin adenine dinucleotide-binding protein that is a key component of the circadian core oscillator complex, which regulates the circadian clock. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been associated with altered sleep patterns. The encoded protein is widely conserved across plants and animals. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]
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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=-0.75).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRY2 | NM_021117.5 | c.*732A>G | 3_prime_UTR_variant | 12/12 | ENST00000616080.2 | ||
CRY2 | NM_001127457.3 | c.*732A>G | 3_prime_UTR_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRY2 | ENST00000616080.2 | c.*732A>G | 3_prime_UTR_variant | 12/12 | 1 | NM_021117.5 | P2 | ||
CRY2 | ENST00000443527.6 | c.*732A>G | 3_prime_UTR_variant | 12/12 | 1 | A2 | |||
CRY2 | ENST00000616623.4 | c.*732A>G | 3_prime_UTR_variant | 12/12 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18158AN: 152096Hom.: 1500 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 20Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 12
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GnomAD4 genome ? AF: 0.119 AC: 18174AN: 152214Hom.: 1504 Cov.: 33 AF XY: 0.119 AC XY: 8839AN XY: 74432
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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