NM_020902.2:c.3113-58G>A

Variant names:

• chr19-7616465-G-A
• rs807812
• NM_020902.2:c.3113-58G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAMSAP3	NM_020902.2	c.3113-58G>A		intron_variant	Intron 13 of 16	ENST00000160298.9	NP_065953.1
CAMSAP3	NM_001080429.3	c.3194-58G>A		intron_variant	Intron 15 of 18		NP_001073898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMSAP3	ENST00000160298.9	c.3113-58G>A		intron_variant	Intron 13 of 16	2	NM_020902.2	ENSP00000160298.3
CAMSAP3	ENST00000446248.4	c.3194-58G>A		intron_variant	Intron 15 of 18	1		ENSP00000416797.1
CAMSAP3	ENST00000593434.1	n.60G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
CAMSAP3	ENST00000595692.1	n.992-58G>A		intron_variant	Intron 2 of 5	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

African (AFR) AF: 0.137 AC: 3428 AN: 25050

American (AMR) AF: 0.134 AC: 5892 AN: 43952

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 3299 AN: 23266

East Asian (EAS) AF: 0.128 AC: 4789 AN: 37342

South Asian (SAS) AF: 0.110 AC: 8559 AN: 77650

European-Finnish (FIN) AF: 0.183 AC: 9502 AN: 51820

Middle Eastern (MID) AF: 0.151 AC: 738 AN: 4888

European-Non Finnish (NFE) AF: 0.196 AC: 142578 AN: 728354

Other (OTH) AF: 0.179 AC: 8271 AN: 46328

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

African (AFR) AF: 0.136 AC: 5656 AN: 41524

American (AMR) AF: 0.147 AC: 2251 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3468

East Asian (EAS) AF: 0.118 AC: 612 AN: 5176

South Asian (SAS) AF: 0.112 AC: 541 AN: 4826

European-Finnish (FIN) AF: 0.168 AC: 1782 AN: 10594

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12983 AN: 67986

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.176 Hom.: 4127

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
PhyloP100		-0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs807812; hg19: chr19-7681351; COSMIC: COSV50382963; COSMIC: COSV50382963;