chr9-135826275-A-G

Position:

• chr9-135826275-A-G

Variant summary

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

The NM_015447.4(CAMSAP1):​c.1223+1132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,262 control chromosomes in the GnomAD database, including 60,067 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 0.89 (59993 hom., cov: 30)
  • Exomes 𝑓: 0.91 (74 hom.)
• Consequence: CAMSAP1 NM_015447.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMSAP1	NM_015447.4	c.1223+1132T>C		intron_variant		ENST00000389532.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMSAP1	ENST00000389532.9	c.1223+1132T>C		intron_variant		5	NM_015447.4	P2
CAMSAP1	ENST00000312405.10	c.389+1132T>C		intron_variant		1
CAMSAP1	ENST00000409386.3	c.1256+1132T>C		intron_variant		5		A2
CAMSAP1	ENST00000483991.5	n.135T>C		non_coding_transcript_exon_variant	1/11	2

Frequencies

GnomAD3 genomes AF: 0.888 AC: 134917 AN: 151968 Hom.: 59942 Cov.: 30

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.873

GnomAD4 exome AF: 0.909 AC: 160 AN: 176 Hom.: 74 Cov.: 0 AF XY: 0.910 AC XY: 111 AN XY: 122

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.899

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.888 AC: 135024 AN: 152086 Hom.: 59993 Cov.: 30 AF XY: 0.888 AC XY: 66016 AN XY: 74332

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.875

Alfa AF: 0.875 Hom.: 31895

Bravo AF: 0.892

Asia WGS AF: 0.964 AC: 3353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.20

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: rs10776851; hg19: chr9-138718121;