dbSNP rs11544766: CAVIN3:p.Ser68Thr (chr11-6320274-C-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_145040.3(CAVIN3):c.203G>C(p.Ser68Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000517 in 1,565,872 control chromosomes in the GnomAD database, including 1 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 0.0027 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00028 ( 1 hom. )

Consequence

CAVIN3
NM_145040.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.868

Variant links:

Genes affected

CAVIN3 (HGNC:9400): (caveolae associated protein 3) The protein encoded by this gene was identified as a binding protein of the protein kinase C, delta (PRKCD). The expression of this gene in cultured cell lines is strongly induced by serum starvation. The expression of this protein was found to be down-regulated in various cancer cell lines, suggesting the possible tumor suppressor function of this protein. [provided by RefSeq, Jul 2008]

CAVIN3 links:

ENSG00000282556 (HGNC:):

ENSG00000282556 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008076578).

BS2

High AC in GnomAd4 at 413 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAVIN3	NM_145040.3 link	c.203G>C	p.Ser68Thr	missense_variant	Exon 1 of 2	ENST00000303927.4	NP_659477.2	Q969G5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAVIN3	ENST00000303927.4 link	c.203G>C	p.Ser68Thr	missense_variant	Exon 1 of 2	1	NM_145040.3	ENSP00000307292.3		Q969G5

Frequencies

GnomAD3 genomes

AF:

0.00271

AC:

413

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00938

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00191

GnomAD2 exomes

AF:

0.000597

AC:

101

AN:

169206

AF XY:

0.000552

show subpopulations

Gnomad AFR exome

AF:

0.00968

Gnomad AMR exome

AF:

0.000280

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000140

Gnomad OTH exome

AF:

0.000645

GnomAD4 exome

AF:

0.000280

AC:

396

AN:

1413526

Hom.:

Cov.:

AF XY:

0.000245

AC XY:

172

AN XY:

700960

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

AC:

332

AN:

32480

Gnomad4 AMR exome

AF:

0.000200

AC:

AN:

39912

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

25480

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

37472

Gnomad4 SAS exome

AF:

0.0000365

AC:

AN:

82206

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

36342

Gnomad4 NFE exome

AF:

0.00000548

AC:

AN:

1095066

Gnomad4 Remaining exome

AF:

0.000747

AC:

AN:

58894

Heterozygous variant carriers

116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00271

AC:

413

AN:

152346

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

183

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.00938

AC:

0.0093768

AN:

0.0093768

Gnomad4 AMR

AF:

0.00105

AC:

0.00104507

AN:

0.00104507

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00

AC:

AN:

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.0000441

AC:

0.0000441021

AN:

0.0000441021

Gnomad4 OTH

AF:

0.00189

AC:

0.00189215

AN:

0.00189215

Heterozygous variant carriers

100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000557

Hom.:

Bravo

AF:

0.00318

ESP6500AA

AF:

0.00707

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000523

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.33

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.079

T;T

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Benign

0.088

LIST_S2

Benign

0.68

T;T

MetaRNN

Benign

0.0081

T;T

MetaSVM

Benign

-0.71

PrimateAI

Uncertain

0.78

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.091

Sift

Benign

0.17

T;T

Sift4G

Pathogenic

0.0

D;D

Polyphen

0.93

P;.

Vest4

0.068

MVP

0.55

MPC

1.1

ClinPred

0.036

GERP RS

4.9

Varity_R

0.28

gMVP

0.28

Mutation Taster

=93/7

polymorphism

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over