6-49846659-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001131.3(CRISP1):c.296G>T(p.Cys99Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000219 in 1,460,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C99S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001131.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRISP1 | NM_001131.3 | c.296G>T | p.Cys99Phe | missense_variant | Exon 5 of 8 | ENST00000335847.9 | NP_001122.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRISP1 | ENST00000335847.9 | c.296G>T | p.Cys99Phe | missense_variant | Exon 5 of 8 | 1 | NM_001131.3 | ENSP00000338276.4 | ||
CRISP1 | ENST00000505118.1 | c.296G>T | p.Cys99Phe | missense_variant | Exon 5 of 8 | 1 | ENSP00000427589.1 | |||
CRISP1 | ENST00000507853.5 | c.296G>T | p.Cys99Phe | missense_variant | Exon 5 of 7 | 1 | ENSP00000425020.1 | |||
CRISP1 | ENST00000329411.9 | c.296G>T | p.Cys99Phe | missense_variant | Exon 4 of 6 | 5 | ENSP00000331317.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250238Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135214
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1460882Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 726722
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at