chr1-200848637-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_203459.4(CAMSAP2):ā€‹c.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

Scores

1
3
15

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 5.77
Variant links:
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]

Genome browser will be placed here

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
CAMSAP2NM_203459.4 linkuse as main transcriptc.1868T>C p.Met623Thr missense_variant 11/17 ENST00000358823.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAMSAP2ENST00000358823.7 linkuse as main transcriptc.1868T>C p.Met623Thr missense_variant 11/175 NM_203459.4 P3Q08AD1-3
CAMSAP2ENST00000236925.8 linkuse as main transcriptc.1901T>C p.Met634Thr missense_variant 12/181 Q08AD1-1
CAMSAP2ENST00000413307.6 linkuse as main transcriptc.1820T>C p.Met607Thr missense_variant 11/171 A2Q08AD1-2
CAMSAP2ENST00000447701.2 linkuse as main transcriptc.395+1345T>C intron_variant, NMD_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.000683
AC:
104
AN:
152194
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000327
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00118
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000490
AC:
123
AN:
250804
Hom.:
0
AF XY:
0.000480
AC XY:
65
AN XY:
135518
show subpopulations
Gnomad AFR exome
AF:
0.000492
Gnomad AMR exome
AF:
0.000521
Gnomad ASJ exome
AF:
0.000895
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000724
Gnomad OTH exome
AF:
0.000328
GnomAD4 exome
AF:
0.000917
AC:
1341
AN:
1461820
Hom.:
2
Cov.:
33
AF XY:
0.000854
AC XY:
621
AN XY:
727204
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.000470
Gnomad4 ASJ exome
AF:
0.000995
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00110
Gnomad4 OTH exome
AF:
0.000811
GnomAD4 genome
AF:
0.000683
AC:
104
AN:
152312
Hom.:
0
Cov.:
32
AF XY:
0.000483
AC XY:
36
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.000327
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00118
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000936
Hom.:
2
Bravo
AF:
0.000638
TwinsUK
AF:
0.000809
AC:
3
ALSPAC
AF:
0.00156
AC:
6
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00163
AC:
14
ExAC
AF:
0.000461
AC:
56
EpiCase
AF:
0.00136
EpiControl
AF:
0.00113

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 providedresearchReproductive Development, Murdoch Childrens Research InstituteJan 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
21
DANN
Benign
0.81
DEOGEN2
Benign
0.046
.;.;T
Eigen
Benign
0.092
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.91
D;D;D
M_CAP
Benign
0.0095
T
MetaRNN
Benign
0.032
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
.;.;L
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
-2.1
N;N;N
REVEL
Benign
0.095
Sift
Benign
0.36
T;T;T
Sift4G
Benign
0.34
T;T;T
Polyphen
0.49
P;B;P
Vest4
0.52
MVP
0.15
MPC
0.45
ClinPred
0.032
T
GERP RS
5.7
Varity_R
0.19
gMVP
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs34958390; hg19: chr1-200817765; API