3-186538713-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_017541.4(CRYGS):c.520C>T(p.Arg174Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R174H) has been classified as Uncertain significance.
Frequency
Consequence
NM_017541.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYGS | NM_017541.4 | c.520C>T | p.Arg174Cys | missense_variant | 3/3 | ENST00000307944.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRYGS | ENST00000307944.6 | c.520C>T | p.Arg174Cys | missense_variant | 3/3 | 1 | NM_017541.4 | P1 | |
CRYGS | ENST00000460288.1 | n.1422C>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
CRYGS | ENST00000392499.6 | c.520C>T | p.Arg174Cys | missense_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251354Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135858
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727236
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2024 | The c.520C>T (p.R174C) alteration is located in exon 3 (coding exon 3) of the CRYGS gene. This alteration results from a C to T substitution at nucleotide position 520, causing the arginine (R) at amino acid position 174 to be replaced by a cysteine (C). 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