chr16-29830629-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005115.5(MVP):c.80G>A(p.Arg27His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,614,034 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0072 ( 14 hom., cov: 31)
Exomes 𝑓: 0.00075 ( 20 hom. )
Consequence
MVP
NM_005115.5 missense
NM_005115.5 missense
Scores
3
13
Clinical Significance
Conservation
PhyloP100: 1.35
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006412536).
BP6
?
Variant 16-29830629-G-A is Benign according to our data. Variant chr16-29830629-G-A is described in ClinVar as [Benign]. Clinvar id is 778608.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00718 (1092/152182) while in subpopulation AFR AF= 0.0251 (1041/41514). AF 95% confidence interval is 0.0238. There are 14 homozygotes in gnomad4. There are 531 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MVP | NM_005115.5 | c.80G>A | p.Arg27His | missense_variant | 2/15 | ENST00000357402.10 | |
MVP | NM_017458.3 | c.80G>A | p.Arg27His | missense_variant | 2/15 | ||
MVP | NM_001293204.1 | c.80G>A | p.Arg27His | missense_variant | 1/14 | ||
MVP | NM_001293205.1 | c.80G>A | p.Arg27His | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MVP | ENST00000357402.10 | c.80G>A | p.Arg27His | missense_variant | 2/15 | 1 | NM_005115.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00720 AC: 1095AN: 152064Hom.: 14 Cov.: 31
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GnomAD3 exomes AF: 0.00206 AC: 517AN: 251304Hom.: 7 AF XY: 0.00136 AC XY: 185AN XY: 135822
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GnomAD4 exome AF: 0.000753 AC: 1101AN: 1461852Hom.: 20 Cov.: 31 AF XY: 0.000619 AC XY: 450AN XY: 727240
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GnomAD4 genome ? AF: 0.00718 AC: 1092AN: 152182Hom.: 14 Cov.: 31 AF XY: 0.00714 AC XY: 531AN XY: 74398
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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 submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;D;D;T;.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;.;T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D;D;D;D;.
Sift
Benign
D;T;T;D;D;T;D;D;.
Sift4G
Uncertain
D;T;T;D;D;D;T;D;D
Polyphen
0.21
.;B;B;.;.;.;.;.;.
Vest4
0.28, 0.29, 0.22
MVP
MPC
0.44
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at