9-135811591-G-C

Variant names:

• chr9-135811591-G-C
• rs147212718
• NM_015447.4:c.4527C>G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_015447.4(CAMSAP1):​c.4527C>G​(p.Ala1509Ala) variant causes a synonymous change. The variant allele was found at a frequency of 0.00686 in 1,592,592 control chromosomes in the GnomAD database, including 56 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 0.0057 (5 hom., cov: 33)
  • Exomes 𝑓: 0.0070 (51 hom.)
• Consequence: CAMSAP1 NM_015447.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.56

Genes affected

CAMSAP1 (HGNC:19946): (calmodulin regulated spectrin associated protein 1) Enables microtubule minus-end binding activity and spectrin binding activity. Involved in several processes, including neuron projection development; regulation of cell morphogenesis; and regulation of microtubule polymerization. Located in microtubule. Colocalizes with microtubule minus-end. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMSAP1	NM_015447.4	c.4527C>G	p.Ala1509Ala	synonymous_variant	Exon 17 of 17	ENST00000389532.9	NP_056262.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMSAP1	ENST00000389532.9	c.4527C>G	p.Ala1509Ala	synonymous_variant	Exon 17 of 17	5	NM_015447.4	ENSP00000374183.4

Frequencies

GnomAD3 genomes AF: 0.00567 AC: 863 AN: 152192 Hom.: 5 Cov.: 33

Gnomad AFR AF: 0.00123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00582

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00864

Gnomad OTH AF: 0.00766

GnomAD3 exomes AF: 0.00625 AC: 1334 AN: 213314 Hom.: 6 AF XY: 0.00642 AC XY: 733 AN XY: 114224

Gnomad AFR exome AF: 0.000831

Gnomad AMR exome AF: 0.00488

Gnomad ASJ exome AF: 0.0161

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00554

Gnomad FIN exome AF: 0.00229

Gnomad NFE exome AF: 0.00835

Gnomad OTH exome AF: 0.0105

GnomAD4 exome AF: 0.00698 AC: 10060 AN: 1440282 Hom.: 51 Cov.: 30 AF XY: 0.00715 AC XY: 5107 AN XY: 714268

Gnomad4 AFR exome AF: 0.000999

Gnomad4 AMR exome AF: 0.00558

Gnomad4 ASJ exome AF: 0.0168

Gnomad4 EAS exome AF: 0.0000257

Gnomad4 SAS exome AF: 0.00543

Gnomad4 FIN exome AF: 0.00236

Gnomad4 NFE exome AF: 0.00752

Gnomad4 OTH exome AF: 0.00781

GnomAD4 genome AF: 0.00567 AC: 863 AN: 152310 Hom.: 5 Cov.: 33 AF XY: 0.00567 AC XY: 422 AN XY: 74478

Gnomad4 AFR AF: 0.00123

Gnomad4 AMR AF: 0.00582

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.00866

Gnomad4 OTH AF: 0.00758

Alfa AF: 0.00753 Hom.: 2

Bravo AF: 0.00569

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CAMSAP1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	7.4
DANN	Benign	0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs147212718; hg19: chr9-138703437;