11-45847449-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The ENST00000443527.6(CRY2):c.22T>C(p.Tyr8His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000763 in 1,442,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000443527.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRY2 | NM_001127457.3 | c.32+168T>C | intron_variant | ||||
CRY2 | NM_021117.5 | upstream_gene_variant | ENST00000616080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRY2 | ENST00000616080.2 | upstream_gene_variant | 1 | NM_021117.5 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000881 AC: 2AN: 226940Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125088
GnomAD4 exome AF: 0.00000763 AC: 11AN: 1442492Hom.: 0 Cov.: 36 AF XY: 0.00000838 AC XY: 6AN XY: 716050
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.22T>C (p.Y8H) alteration is located in exon 1 (coding exon 1) of the CRY2 gene. This alteration results from a T to C substitution at nucleotide position 22, causing the tyrosine (Y) at amino acid position 8 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at