dbSNP rs2292096: CAMSAP2:c.4132-113A>C (chr1-200857641-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_203459.4(CAMSAP2):c.4132-113A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000116 in 864,806 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000012 ( 0 hom. )

Consequence

CAMSAP2
NM_203459.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.138

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMSAP2	NM_203459.4 link	c.4132-113A>C		intron_variant	Intron 16 of 16	ENST00000358823.7	NP_982284.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CAMSAP2	ENST00000358823.7 link	c.4132-113A>C	intron_variant	Intron 16 of 16	5	NM_203459.4	ENSP00000351684.2
CAMSAP2	ENST00000236925.9 link	c.4165-113A>C	intron_variant	Intron 17 of 17	1		ENSP00000236925.4
CAMSAP2	ENST00000413307.6 link	c.4084-113A>C	intron_variant	Intron 16 of 16	1		ENSP00000416800.2
CAMSAP2	ENST00000475326.1 link	c.*199A>C	3_prime_UTR_variant	Exon 2 of 2	5		ENSP00000434766.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000116

AC:

AN:

864806

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

437606

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

19740

American (AMR)

AF:

0.00

AC:

AN:

19522

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16496

East Asian (EAS)

AF:

0.00

AC:

AN:

33772

South Asian (SAS)

AF:

0.00

AC:

AN:

52158

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42086

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3952

European-Non Finnish (NFE)

AF:

0.00000157

AC:

AN:

637760

Other (OTH)

AF:

0.00

AC:

AN:

39320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

(source)

DANN

Benign

0.48

PhyloP100

0.14

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over