Genetic Variant CAMSAP2:c.4132-113A>G (chr1-200857641-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_203459.4(CAMSAP2):c.4132-113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,016,006 control chromosomes in the GnomAD database, including 7,734 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1562 hom., cov: 33)

Exomes 𝑓: 0.12 ( 6172 hom. )

Consequence

CAMSAP2
NM_203459.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.138

Publications

29 publications found

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]

CAMSAP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203459.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CAMSAP2	NM_203459.4	MANE Select	c.4132-113A>G	intron	N/A	NP_982284.1
CAMSAP2	NM_001297707.3		c.4165-113A>G	intron	N/A	NP_001284636.1
CAMSAP2	NM_001389638.1		c.4117-113A>G	intron	N/A	NP_001376567.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CAMSAP2	ENST00000358823.7	TSL:5 MANE Select	c.4132-113A>G	intron	N/A	ENSP00000351684.2
CAMSAP2	ENST00000236925.9	TSL:1	c.4165-113A>G	intron	N/A	ENSP00000236925.4
CAMSAP2	ENST00000413307.6	TSL:1	c.4084-113A>G	intron	N/A	ENSP00000416800.2

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21140

AN:

152066

Hom.:

1560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.0622

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.117

AC:

101108

AN:

863822

Hom.:

6172

Cov.:

AF XY:

0.116

AC XY:

50734

AN XY:

437130

show subpopulations

African (AFR)

AF:

0.184

AC:

3622

AN:

19708

American (AMR)

AF:

0.135

AC:

2628

AN:

19510

Ashkenazi Jewish (ASJ)

AF:

0.0664

AC:

1094

AN:

16486

East Asian (EAS)

AF:

0.160

AC:

5384

AN:

33744

South Asian (SAS)

AF:

0.101

AC:

5243

AN:

52116

European-Finnish (FIN)

AF:

0.134

AC:

5646

AN:

42064

Middle Eastern (MID)

AF:

0.0932

AC:

368

AN:

3948

European-Non Finnish (NFE)

AF:

0.114

AC:

72506

AN:

636968

Other (OTH)

AF:

0.118

AC:

4617

AN:

39278

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4553

9106

13658

18211

22764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2266

4532

6798

9064

11330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.139

AC:

21170

AN:

152184

Hom.:

1562

Cov.:

AF XY:

0.139

AC XY:

10356

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.186

AC:

7712

AN:

41506

American (AMR)

AF:

0.138

AC:

2108

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0622

AC:

216

AN:

3470

East Asian (EAS)

AF:

0.171

AC:

889

AN:

5184

South Asian (SAS)

AF:

0.103

AC:

496

AN:

4826

European-Finnish (FIN)

AF:

0.134

AC:

1425

AN:

10600

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7839

AN:

67988

Other (OTH)

AF:

0.125

AC:

264

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

941

1881

2822

3762

4703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.116

Hom.:

3360

Bravo

AF:

0.144

Asia WGS

AF:

0.146

AC:

505

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.4

(source)

DANN

Benign

0.46

PhyloP100

0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over