8-75020070-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031461.6(CRISPLD1):c.1235A>G(p.His412Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,726 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
CRISPLD1
NM_031461.6 missense
NM_031461.6 missense
Scores
7
11
1
Clinical Significance
Conservation
PhyloP100: 7.13
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRISPLD1 | NM_031461.6 | c.1235A>G | p.His412Arg | missense_variant | 12/15 | ENST00000262207.9 | |
CRISPLD1 | NM_001286777.2 | c.677A>G | p.His226Arg | missense_variant | 10/13 | ||
CRISPLD1 | NM_001286778.2 | c.671A>G | p.His224Arg | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRISPLD1 | ENST00000262207.9 | c.1235A>G | p.His412Arg | missense_variant | 12/15 | 1 | NM_031461.6 | P1 | |
CRISPLD1 | ENST00000517786.1 | c.677A>G | p.His226Arg | missense_variant | 10/13 | 2 | |||
CRISPLD1 | ENST00000523524.5 | c.671A>G | p.His224Arg | missense_variant | 11/14 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251384Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135854
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727182
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GnomAD4 genome ? Cov.: 32
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Cov.:
32
ExAC
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1
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2021 | The c.1235A>G (p.H412R) alteration is located in exon 12 (coding exon 11) of the CRISPLD1 gene. This alteration results from a A to G substitution at nucleotide position 1235, causing the histidine (H) at amino acid position 412 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;T;D
Polyphen
D;.;.
Vest4
MutPred
Loss of methylation at K408 (P = 0.0814);.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at