6-49846593-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001131.3(CRISP1):c.362G>A(p.Ser121Asn) 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 1,613,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. S121I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001131.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRISP1 | NM_001131.3 | c.362G>A | p.Ser121Asn | 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.362G>A | p.Ser121Asn | missense_variant | Exon 5 of 8 | 1 | NM_001131.3 | ENSP00000338276.4 | ||
CRISP1 | ENST00000505118.1 | c.362G>A | p.Ser121Asn | missense_variant | Exon 5 of 8 | 1 | ENSP00000427589.1 | |||
CRISP1 | ENST00000507853.5 | c.362G>A | p.Ser121Asn | missense_variant | Exon 5 of 7 | 1 | ENSP00000425020.1 | |||
CRISP1 | ENST00000329411.9 | c.362G>A | p.Ser121Asn | missense_variant | Exon 4 of 6 | 5 | ENSP00000331317.5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251036Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135672
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461318Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 726956
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74452
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at