1-200857641-A-G

Position:

• chr1-200857641-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMSAP2	NM_203459.4	c.4132-113A>G		intron_variant		ENST00000358823.7	NP_982284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMSAP2	ENST00000358823.7	c.4132-113A>G		intron_variant		5	NM_203459.4	ENSP00000351684	P3
CAMSAP2	ENST00000236925.8	c.4165-113A>G		intron_variant		1		ENSP00000236925
CAMSAP2	ENST00000413307.6	c.4084-113A>G		intron_variant		1		ENSP00000416800	A2
CAMSAP2	ENST00000475326.1	c.*199A>G		3_prime_UTR_variant	2/2	5		ENSP00000434766

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21140 AN: 152066 Hom.: 1560 Cov.: 33

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.: 11 AF XY: 0.116 AC XY: 50734 AN XY: 437130

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.135

Gnomad4 ASJ exome AF: 0.0664

Gnomad4 EAS exome AF: 0.160

Gnomad4 SAS exome AF: 0.101

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.139 AC: 21170 AN: 152184 Hom.: 1562 Cov.: 33 AF XY: 0.139 AC XY: 10356 AN XY: 74414

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.125

Alfa AF: 0.112 Hom.: 1260

Bravo AF: 0.144

Asia WGS AF: 0.146 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs2292096; hg19: chr1-200826769;