2-218362876-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198559.2(CATIP):c.604G>A(p.Glu202Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 1,613,696 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0026 ( 7 hom. )
Consequence
CATIP
NM_198559.2 missense
NM_198559.2 missense
Scores
10
8
Clinical Significance
Conservation
PhyloP100: 2.81
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.02474609).
BP6
Variant 2-218362876-G-A is Benign according to our data. Variant chr2-218362876-G-A is described in ClinVar as [Benign]. Clinvar id is 3770423.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00171 AC: 260AN: 152194Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00136 AC: 341AN: 250662Hom.: 0 AF XY: 0.00148 AC XY: 200AN XY: 135484
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GnomAD4 exome AF: 0.00264 AC: 3852AN: 1461384Hom.: 7 Cov.: 31 AF XY: 0.00253 AC XY: 1842AN XY: 727000
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GnomAD4 genome AF: 0.00171 AC: 260AN: 152312Hom.: 0 Cov.: 31 AF XY: 0.00144 AC XY: 107AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
CATIP: BP4, BS1, BS2 -
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
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
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