chr12-106999695-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_004075.5(CRY1):c.993G>A(p.Ala331Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,614,240 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004075.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00111 AC: 169AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000259 AC: 65AN: 251396Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135890
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727246
GnomAD4 genome AF: 0.00117 AC: 178AN: 152348Hom.: 2 Cov.: 32 AF XY: 0.00106 AC XY: 79AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
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CRY1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at