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GeneBe

2-191836682-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_004657.6(CAVIN2):c.519A>G(p.Lys173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 1,613,768 control chromosomes in the GnomAD database, including 242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 121 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 121 hom. )

Consequence

CAVIN2
NM_004657.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.433
Variant links:
Genes affected
CAVIN2 (HGNC:10690): (caveolae associated protein 2) This gene encodes a calcium-independent phospholipid-binding protein whose expression increases in serum-starved cells. This protein is a substrate for protein kinase C (PKC) phosphorylation and recruits polymerase I and transcript release factor (PTRF) to caveolae. Removal of this protein causes caveolae loss and its over-expression results in caveolae deformation and membrane tubulation.[provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 2-191836682-T-C is Benign according to our data. Variant chr2-191836682-T-C is described in ClinVar as [Benign]. Clinvar id is 782418.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.433 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CAVIN2NM_004657.6 linkuse as main transcriptc.519A>G p.Lys173= synonymous_variant 2/2 ENST00000304141.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAVIN2ENST00000304141.5 linkuse as main transcriptc.519A>G p.Lys173= synonymous_variant 2/21 NM_004657.6 P1

Frequencies

GnomAD3 genomes
AF:
0.0227
AC:
3460
AN:
152132
Hom.:
122
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0794
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00766
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0163
GnomAD3 exomes
AF:
0.00570
AC:
1425
AN:
249852
Hom.:
62
AF XY:
0.00429
AC XY:
581
AN XY:
135516
show subpopulations
Gnomad AFR exome
AF:
0.0818
Gnomad AMR exome
AF:
0.00304
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000262
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000186
Gnomad OTH exome
AF:
0.00346
GnomAD4 exome
AF:
0.00226
AC:
3303
AN:
1461518
Hom.:
121
Cov.:
33
AF XY:
0.00191
AC XY:
1386
AN XY:
727026
show subpopulations
Gnomad4 AFR exome
AF:
0.0802
Gnomad4 AMR exome
AF:
0.00345
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000118
Gnomad4 OTH exome
AF:
0.00508
GnomAD4 genome
AF:
0.0228
AC:
3467
AN:
152250
Hom.:
121
Cov.:
32
AF XY:
0.0224
AC XY:
1668
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0794
Gnomad4 AMR
AF:
0.00765
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0161
Alfa
AF:
0.0104
Hom.:
33
Bravo
AF:
0.0259
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 21, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
Cadd
Benign
3.3
Dann
Benign
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs61742216; hg19: chr2-192701408; API