1-200857641-A-C

Variant names:

• chr1-200857641-A-C
• rs2292096
• NM_203459.4:c.4132-113A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 0 publications found

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]

ACMG classification

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).

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000116 AC: 1 AN: 864806 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 437606

African (AFR) AF: 0.00 AC: 0 AN: 19740

American (AMR) AF: 0.00 AC: 0 AN: 19522

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16496

East Asian (EAS) AF: 0.00 AC: 0 AN: 33772

South Asian (SAS) AF: 0.00 AC: 0 AN: 52158

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42086

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3952

European-Non Finnish (NFE) AF: 0.00000157 AC: 1 AN: 637760

Other (OTH) AF: 0.00 AC: 0 AN: 39320

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
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

Other links and lift over

dbSNP: rs2292096; hg19: chr1-200826769;