Variant 16-29830909-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_005115.5(MVP):c.157G>A(p.Val53Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000241 in 1,613,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

MVP
NM_005115.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.04

Variant links:

Genes affected

MVP (HGNC:7531): (major vault protein) This gene encodes the major component of the vault complex. Vaults are multi-subunit ribonucleoprotein structures that may be involved in nucleo-cytoplasmic transport. The encoded protein may play a role in multiple cellular processes by regulating the MAP kinase, JAK/STAT and phosphoinositide 3-kinase/Akt signaling pathways. The encoded protein also plays a role in multidrug resistance, and expression of this gene may be a prognostic marker for several types of cancer. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2012]

MVP links:

MVP (HGNC:):

MVP links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.008913785).

BP6

Variant 16-29830909-G-A is Benign according to our data. Variant chr16-29830909-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 731123.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MVP	NM_005115.5 linkuse as main transcript	c.157G>A	p.Val53Ile	missense_variant	3/15	ENST00000357402.10	NP_005106.2	Q14764X5D2M8
MVP	NM_017458.3 linkuse as main transcript	c.157G>A	p.Val53Ile	missense_variant	3/15		NP_059447.2	Q14764X5D2M8
MVP	NM_001293204.1 linkuse as main transcript	c.157G>A	p.Val53Ile	missense_variant	2/14		NP_001280133.1	Q14764X5DNU0
MVP	NM_001293205.1 linkuse as main transcript	c.157G>A	p.Val53Ile	missense_variant	2/13		NP_001280134.1	Q14764X5D7K9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MVP	ENST00000357402.10 linkuse as main transcript	c.157G>A	p.Val53Ile	missense_variant	3/15	1	NM_005115.5	ENSP00000349977.5		Q14764

Frequencies

GnomAD3 genomes

AF:

0.00120

AC:

182

AN:

151908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.000339

AC:

AN:

250720

Hom.:

AF XY:

0.000295

AC XY:

AN XY:

135450

show subpopulations

Gnomad AFR exome

AF:

0.00394

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000972

Gnomad OTH exome

AF:

0.000327

GnomAD4 exome

AF:

0.000141

AC:

206

AN:

1461066

Hom.:

Cov.:

AF XY:

0.000132

AC XY:

AN XY:

726674

show subpopulations

Gnomad4 AFR exome

AF:

0.00371

Gnomad4 AMR exome

AF:

0.000112

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000612

Gnomad4 OTH exome

AF:

0.000116

GnomAD4 genome

AF:

0.00120

AC:

182

AN:

152026

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.00410

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000103

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.000263

Hom.:

Bravo

AF:

0.00130

ESP6500AA

AF:

0.00387

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.000420

AC:

EpiCase

AF:

0.000109

EpiControl

AF:

0.0000593

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 16, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.015

T;T;T;T;.;.;T

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.23

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.81

T;T;.;T;T;T;T

M_CAP

Benign

0.0076

MetaRNN

Benign

0.0089

T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

.;L;L;.;.;.;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.21

N;N;N;N;N;N;N

REVEL

Benign

0.039

Sift

Benign

0.54

T;T;T;T;T;T;T

Sift4G

Benign

0.83

T;T;T;T;T;T;T

Polyphen

0.048

.;B;B;.;.;.;.

Vest4

0.25

MVP

0.20

MPC

0.29

ClinPred

0.0094

GERP RS

3.6

Varity_R

0.036

gMVP

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over