chr2-218362876-G-A

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

Scores

10
8

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.81
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CATIPNM_198559.2 linkc.604G>A p.Glu202Lys missense_variant Exon 6 of 10 ENST00000289388.4 NP_940961.1 Q7Z7H3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CATIPENST00000289388.4 linkc.604G>A p.Glu202Lys missense_variant Exon 6 of 10 1 NM_198559.2 ENSP00000289388.3 Q7Z7H3
CATIPENST00000481940.1 linkn.226+2217G>A intron_variant Intron 3 of 5 3

Frequencies

GnomAD3 genomes
AF:
0.00171
AC:
260
AN:
152194
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000579
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00229
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000282
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00287
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00136
AC:
341
AN:
250662
Hom.:
0
AF XY:
0.00148
AC XY:
200
AN XY:
135484
show subpopulations
Gnomad AFR exome
AF:
0.000677
Gnomad AMR exome
AF:
0.000840
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.000469
Gnomad NFE exome
AF:
0.00246
Gnomad OTH exome
AF:
0.00180
GnomAD4 exome
AF:
0.00264
AC:
3852
AN:
1461384
Hom.:
7
Cov.:
31
AF XY:
0.00253
AC XY:
1842
AN XY:
727000
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.00110
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.000358
Gnomad4 NFE exome
AF:
0.00326
Gnomad4 OTH exome
AF:
0.00235
GnomAD4 genome
AF:
0.00171
AC:
260
AN:
152312
Hom.:
0
Cov.:
31
AF XY:
0.00144
AC XY:
107
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.000577
Gnomad4 AMR
AF:
0.00229
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000282
Gnomad4 NFE
AF:
0.00287
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00208
Hom.:
1
Bravo
AF:
0.00189
TwinsUK
AF:
0.00512
AC:
19
ALSPAC
AF:
0.00234
AC:
9
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00279
AC:
24
ExAC
AF:
0.00137
AC:
166
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00305
EpiControl
AF:
0.00344

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.22
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.092
T
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.82
T
M_CAP
Benign
0.057
D
MetaRNN
Benign
0.025
T
MetaSVM
Uncertain
-0.17
T
MutationAssessor
Uncertain
2.4
M
PROVEAN
Uncertain
-2.7
D
REVEL
Uncertain
0.48
Sift
Uncertain
0.014
D
Sift4G
Uncertain
0.010
D
Polyphen
1.0
D
Vest4
0.35
MVP
0.64
MPC
0.73
ClinPred
0.021
T
GERP RS
3.8
Varity_R
0.24
gMVP
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138318485; hg19: chr2-219227599; API