Variant rs1051992 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145040.3(CAVIN3):c.473T>C(p.Leu158Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 1,606,178 control chromosomes in the GnomAD database, including 239,745 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.51 ( 20612 hom., cov: 34)

Exomes 𝑓: 0.55 ( 219133 hom. )

Consequence

CAVIN3
NM_145040.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

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:

LOC101927825 (HGNC:):

LOC101927825 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.296233E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAVIN3	NM_145040.3 linkuse as main transcript	c.473T>C	p.Leu158Pro	missense_variant	2/2	ENST00000303927.4
LOC101927825	XR_007062569.1 linkuse as main transcript	n.336A>G		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAVIN3	ENST00000303927.4 linkuse as main transcript	c.473T>C	p.Leu158Pro	missense_variant	2/2	1	NM_145040.3	P1

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78272

AN:

152032

Hom.:

20604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.644

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.498

GnomAD3 exomes

AF:

0.550

AC:

130009

AN:

236392

Hom.:

36196

AF XY:

0.559

AC XY:

72538

AN XY:

129648

show subpopulations

Gnomad AFR exome

AF:

0.389

Gnomad AMR exome

AF:

0.455

Gnomad ASJ exome

AF:

0.527

Gnomad EAS exome

AF:

0.648

Gnomad SAS exome

AF:

0.614

Gnomad FIN exome

AF:

0.639

Gnomad NFE exome

AF:

0.555

Gnomad OTH exome

AF:

0.547

GnomAD4 exome

AF:

0.547

AC:

795125

AN:

1454026

Hom.:

219133

Cov.:

AF XY:

0.550

AC XY:

397635

AN XY:

723450

show subpopulations

Gnomad4 AFR exome

AF:

0.388

Gnomad4 AMR exome

AF:

0.463

Gnomad4 ASJ exome

AF:

0.535

Gnomad4 EAS exome

AF:

0.612

Gnomad4 SAS exome

AF:

0.612

Gnomad4 FIN exome

AF:

0.640

Gnomad4 NFE exome

AF:

0.545

Gnomad4 OTH exome

AF:

0.537

GnomAD4 genome

AF:

0.515

AC:

78313

AN:

152152

Hom.:

20612

Cov.:

AF XY:

0.520

AC XY:

38703

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.507

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.602

Gnomad4 FIN

AF:

0.644

Gnomad4 NFE

AF:

0.551

Gnomad4 OTH

AF:

0.495

Alfa

AF:

0.547

Hom.:

50015

Bravo

AF:

0.494

TwinsUK

AF:

0.536

AC:

1988

ALSPAC

AF:

0.545

AC:

2101

ESP6500AA

AF:

0.396

AC:

1736

ESP6500EA

AF:

0.540

AC:

4636

ExAC

AF:

0.549

AC:

66493

Asia WGS

AF:

0.579

AC:

2018

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.036

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

Cadd

Benign

3.6

Dann

Benign

0.62

DEOGEN2

Benign

0.027

T;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0038

LIST_S2

Benign

0.41

T;T

MetaRNN

Benign

0.0000033

T;T

MetaSVM

Benign

-0.93

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.38

PROVEAN

Benign

0.19

N;N

REVEL

Benign

0.023

Sift

Benign

0.26

T;T

Sift4G

Benign

0.31

T;T

Polyphen

0.0

B;.

Vest4

0.093

MPC

0.57

ClinPred

0.0056

GERP RS

-3.6

Varity_R

0.10

gMVP

0.039

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