rs3824354

chr9-135827810-G-Cchr9-135827810-G-T

Variant summary

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

The NM_015447.4(CAMSAP1):c.1046-226C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,228 control chromosomes in the GnomAD database, including 980 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 0.099 (980 hom., cov: 33)
• Consequence: CAMSAP1 NM_015447.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMSAP1	NM_015447.4	c.1046-226C>G		intron_variant		ENST00000389532.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMSAP1	ENST00000389532.9	c.1046-226C>G		intron_variant		5	NM_015447.4	P2
CAMSAP1	ENST00000312405.10	c.212-226C>G		intron_variant		1
CAMSAP1	ENST00000409386.3	c.1079-226C>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15113 AN: 152110 Hom.: 981 Cov.: 33

Gnomad AFR AF: 0.0937

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0841

Gnomad OTH AF: 0.0923

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0994 AC: 15125 AN: 152228 Hom.: 980 Cov.: 33 AF XY: 0.103 AC XY: 7682 AN XY: 74434

Gnomad4 AFR AF: 0.0937

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0841

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0466 Hom.: 40

Bravo AF: 0.0996

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.083
Dann	Benign	0.76

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: rs3824354; hg19: chr9-138719656;