chr1-200848637-T-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_203459.4(CAMSAP2):āc.1868T>Cā(p.Met623Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000895 in 1,614,132 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: š 0.00068 ( 0 hom., cov: 32)
Exomes š: 0.00092 ( 2 hom. )
Consequence
CAMSAP2
NM_203459.4 missense
NM_203459.4 missense
Scores
1
3
15
Clinical Significance
Conservation
PhyloP100: 5.77
Genes affected
CAMSAP2 (HGNC:29188): (calmodulin regulated spectrin associated protein family member 2) Enables microtubule minus-end binding activity. Involved in several processes, including axon development; regulation of dendrite development; and regulation of organelle organization. Located in cytosol and microtubule end. Colocalizes with Golgi apparatus; centrosome; and microtubule minus-end. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.032067448).
BS2
High AC in GnomAd4 at 104 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMSAP2 | NM_203459.4 | c.1868T>C | p.Met623Thr | missense_variant | 11/17 | ENST00000358823.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMSAP2 | ENST00000358823.7 | c.1868T>C | p.Met623Thr | missense_variant | 11/17 | 5 | NM_203459.4 | P3 | |
CAMSAP2 | ENST00000236925.8 | c.1901T>C | p.Met634Thr | missense_variant | 12/18 | 1 | |||
CAMSAP2 | ENST00000413307.6 | c.1820T>C | p.Met607Thr | missense_variant | 11/17 | 1 | A2 | ||
CAMSAP2 | ENST00000447701.2 | c.395+1345T>C | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000683 AC: 104AN: 152194Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000490 AC: 123AN: 250804Hom.: 0 AF XY: 0.000480 AC XY: 65AN XY: 135518
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GnomAD4 exome AF: 0.000917 AC: 1341AN: 1461820Hom.: 2 Cov.: 33 AF XY: 0.000854 AC XY: 621AN XY: 727204
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GnomAD4 genome AF: 0.000683 AC: 104AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74484
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Premature ovarian insufficiency Uncertain:1
Uncertain significance, no assertion criteria provided | research | Reproductive Development, Murdoch Childrens Research Institute | Jan 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;.;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;B;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
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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