rs3815824
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005115.5(MVP):c.1192-57C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,518,102 control chromosomes in the GnomAD database, including 16,509 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 0.16 ( 2157 hom., cov: 31)
Exomes 𝑓: 0.14 ( 14352 hom. )
Consequence
MVP
NM_005115.5 intron
NM_005115.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.771
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MVP | NM_005115.5 | c.1192-57C>T | intron_variant | ENST00000357402.10 | |||
MVP | NM_001293204.1 | c.1192-57C>T | intron_variant | ||||
MVP | NM_001293205.1 | c.1192-57C>T | intron_variant | ||||
MVP | NM_017458.3 | c.1192-57C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MVP | ENST00000357402.10 | c.1192-57C>T | intron_variant | 1 | NM_005115.5 | P1 | |||
MVP | ENST00000395353.5 | c.1192-57C>T | intron_variant | 5 | P1 | ||||
MVP | ENST00000563558.5 | c.379-57C>T | intron_variant | 4 | |||||
MVP | ENST00000568068.1 | n.367-57C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24391AN: 151836Hom.: 2145 Cov.: 31
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GnomAD4 exome AF: 0.141 AC: 192557AN: 1366148Hom.: 14352 AF XY: 0.141 AC XY: 94015AN XY: 669068
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GnomAD4 genome ? AF: 0.161 AC: 24445AN: 151954Hom.: 2157 Cov.: 31 AF XY: 0.156 AC XY: 11591AN XY: 74278
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at