chr7-36333889-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001199706.2(MATCAP2):c.1264G>A(p.Ala422Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
MATCAP2
NM_001199706.2 missense
NM_001199706.2 missense
Scores
8
6
5
Clinical Significance
Conservation
PhyloP100: 5.57
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MATCAP2 | NM_001199706.2 | c.1264G>A | p.Ala422Thr | missense_variant | 5/7 | ENST00000440378.6 | NP_001186635.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MATCAP2 | ENST00000440378.6 | c.1264G>A | p.Ala422Thr | missense_variant | 5/7 | 1 | NM_001199706.2 | ENSP00000390837 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248870Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135022
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461450Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726990
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152320Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74486
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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 | Sep 29, 2023 | The c.1273G>A (p.A425T) alteration is located in exon 5 (coding exon 5) of the KIAA0895 gene. This alteration results from a G to A substitution at nucleotide position 1273, causing the alanine (A) at amino acid position 425 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
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.;.;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
M;.;.;.;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Uncertain
D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
D;D;D;D;T;T
Sift4G
Uncertain
D;D;D;T;T;T
Polyphen
D;D;D;.;.;.
Vest4
MutPred
Gain of phosphorylation at A425 (P = 0.0412);.;.;.;.;.;
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