chr16-84849390-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031476.4(CRISPLD2):c.365G>A(p.Arg122His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,612,488 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R122R) has been classified as Likely benign.
Frequency
Consequence
NM_031476.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRISPLD2 | NM_031476.4 | c.365G>A | p.Arg122His | missense_variant | 4/15 | ENST00000262424.10 | |
CRISPLD2 | XM_005256190.2 | c.365G>A | p.Arg122His | missense_variant | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRISPLD2 | ENST00000262424.10 | c.365G>A | p.Arg122His | missense_variant | 4/15 | 1 | NM_031476.4 | P4 | |
ENST00000648152.1 | n.373-556C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250778Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135500
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1460280Hom.: 0 Cov.: 41 AF XY: 0.0000289 AC XY: 21AN XY: 726194
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.365G>A (p.R122H) alteration is located in exon 4 (coding exon 3) of the CRISPLD2 gene. This alteration results from a G to A substitution at nucleotide position 365, causing the arginine (R) at amino acid position 122 to be replaced by a histidine (H). 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