chr2-29135586-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024692.6(CLIP4):āc.568G>Cā(p.Ala190Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,458,108 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
CLIP4
NM_024692.6 missense
NM_024692.6 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 6.64
Genes affected
CLIP4 (HGNC:26108): (CAP-Gly domain containing linker protein family member 4) Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Located in intracellular membrane-bounded organelle. [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
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458108Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725258
GnomAD4 exome
AF:
AC:
2
AN:
1458108
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
725258
Gnomad4 AFR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 | Dec 10, 2024 | The c.568G>C (p.A190P) alteration is located in exon 6 (coding exon 5) of the CLIP4 gene. This alteration results from a G to C substitution at nucleotide position 568, causing the alanine (A) at amino acid position 190 to be replaced by a proline (P). 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
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T;.;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;.;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N;N;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.28
.;.;B;B;.;.
Vest4
MutPred
Loss of catalytic residue at A190 (P = 0.0077);.;Loss of catalytic residue at A190 (P = 0.0077);Loss of catalytic residue at A190 (P = 0.0077);Loss of catalytic residue at A190 (P = 0.0077);.;
MVP
MPC
0.23
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 16
Find out detailed SpliceAI scores and Pangolin per-transcript scores at