rs807812

Positions:

• chr19-7616465-G-A
• chr19-7616465-G-C
• chr19-7616465-G-T

Variant summary

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

The NM_020902.2(CAMSAP3):​c.3113-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,190,828 control chromosomes in the GnomAD database, including 19,989 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 0.16 (2183 hom., cov: 32)
  • Exomes 𝑓: 0.18 (17806 hom.)
• Consequence: CAMSAP3 NM_020902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

Genes affected

CAMSAP3 (HGNC:29307): (calmodulin regulated spectrin associated protein family member 3) Enables actin filament binding activity and microtubule minus-end binding activity. Involved in several processes, including microtubule cytoskeleton organization; regulation of organelle organization; and zonula adherens maintenance. Located in cytoplasm; nucleoplasm; and zonula adherens. Colocalizes with 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMSAP3	NM_020902.2	c.3113-58G>A		intron_variant		ENST00000160298.9
CAMSAP3	NM_001080429.3	c.3194-58G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMSAP3	ENST00000160298.9	c.3113-58G>A		intron_variant		2	NM_020902.2	A2
CAMSAP3	ENST00000446248.4	c.3194-58G>A		intron_variant		1		P3
CAMSAP3	ENST00000593434.1	n.60G>A		non_coding_transcript_exon_variant	1/2	3
CAMSAP3	ENST00000595692.1	n.992-58G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25078 AN: 152060 Hom.: 2182 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.180 AC: 187056 AN: 1038650 Hom.: 17806 Cov.: 14 AF XY: 0.177 AC XY: 94752 AN XY: 534980

Gnomad4 AFR exome AF: 0.137

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.128

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.183

Gnomad4 NFE exome AF: 0.196

Gnomad4 OTH exome AF: 0.179

GnomAD4 genome AF: 0.165 AC: 25087 AN: 152178 Hom.: 2183 Cov.: 32 AF XY: 0.162 AC XY: 12079 AN XY: 74410

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.159

Alfa AF: 0.175 Hom.: 3247

Bravo AF: 0.165

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs807812; hg19: chr19-7681351; COSMIC: COSV50382963; COSMIC: COSV50382963;