11-45860978-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_021117.5(CRY2):c.598G>A(p.Glu200Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,856 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021117.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152240Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250432Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135462
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461616Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727098
GnomAD4 genome AF: 0.000289 AC: 44AN: 152240Hom.: 1 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.661G>A (p.E221K) alteration is located in exon 4 (coding exon 4) of the CRY2 gene. This alteration results from a G to A substitution at nucleotide position 661, causing the glutamic acid (E) at amino acid position 221 to be replaced by a lysine (K). 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