Genetic Variant NM_020902.2:c.331A>G (chr19-7605408-A-G) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020902.2(CAMSAP3):c.331A>G(p.Arg111Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CAMSAP3
NM_020902.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.63

Publications

0 publications found

Variant links:

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]

CAMSAP3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020902.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMSAP3	NM_020902.2	MANE Select	c.331A>G	p.Arg111Gly	missense	Exon 2 of 17	NP_065953.1	Q9P1Y5-1
	CAMSAP3	NM_001080429.3		c.331A>G	p.Arg111Gly	missense	Exon 2 of 19	NP_001073898.1	Q9P1Y5-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CAMSAP3	ENST00000160298.9	TSL:2 MANE Select	c.331A>G	p.Arg111Gly	missense	Exon 2 of 17	ENSP00000160298.3	Q9P1Y5-1
CAMSAP3	ENST00000446248.4	TSL:1	c.331A>G	p.Arg111Gly	missense	Exon 2 of 19	ENSP00000416797.1	Q9P1Y5-2
CAMSAP3	ENST00000930508.1		c.331A>G	p.Arg111Gly	missense	Exon 2 of 17	ENSP00000600567.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1360752

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

668316

African (AFR)

AF:

0.00

AC:

AN:

29482

American (AMR)

AF:

0.00

AC:

AN:

31264

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21366

East Asian (EAS)

AF:

0.00

AC:

AN:

35324

South Asian (SAS)

AF:

0.00

AC:

AN:

74658

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50574

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5298

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1057122

Other (OTH)

AF:

0.00

AC:

AN:

55664

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.30

BayesDel_addAF

Benign

-0.054

BayesDel_noAF

Benign

-0.32

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.22

Eigen

Uncertain

0.28

Eigen_PC

Benign

0.20

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.85

M_CAP

Benign

0.036

MetaRNN

Uncertain

0.63

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

PhyloP100

2.6

PrimateAI

Uncertain

0.60

PROVEAN

Pathogenic

-4.5

REVEL

Benign

0.15

Sift

Uncertain

0.0060

Sift4G

Uncertain

0.0090

Polyphen

0.98

Vest4

0.64

MutPred

0.40

Loss of stability (P = 0.008)

MVP

0.41

MPC

1.4

ClinPred

0.98

GERP RS

3.4

Varity_R

0.29

gMVP

0.72

Mutation Taster

=79/21

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over