2-218367842-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198559.2(CATIP):c.1042G>A(p.Ala348Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,104 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
CATIP
NM_198559.2 missense
NM_198559.2 missense
Scores
9
9
Clinical Significance
Conservation
PhyloP100: 3.21
Genes affected
CATIP (HGNC:25062): (ciliogenesis associated TTC17 interacting protein) Involved in actin filament polymerization and cilium organization. Located in several cellular components, including actin cytoskeleton; nucleus; and plasma membrane. Implicated in spermatogenic failure. [provided by Alliance of Genome Resources, Apr 2022]
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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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CATIP | NM_198559.2 | c.1042G>A | p.Ala348Thr | missense_variant | 10/10 | ENST00000289388.4 | NP_940961.1 | |
CATIP-AS1 | NR_110573.1 | n.61C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CATIP | ENST00000289388.4 | c.1042G>A | p.Ala348Thr | missense_variant | 10/10 | 1 | NM_198559.2 | ENSP00000289388 | P1 | |
CATIP-AS1 | ENST00000441749.2 | n.44C>T | non_coding_transcript_exon_variant | 1/3 | 1 | |||||
CATIP | ENST00000481940.1 | n.513G>A | non_coding_transcript_exon_variant | 6/6 | 3 | |||||
CATIP | ENST00000494447.1 | n.2132G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248194Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134950
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460754Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726744
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74498
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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 | May 26, 2022 | The c.1042G>A (p.A348T) alteration is located in exon 10 (coding exon 10) of the CATIP gene. This alteration results from a G to A substitution at nucleotide position 1042, causing the alanine (A) at amino acid position 348 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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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