chr5-170862025-C-A
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_022897.5(RANBP17):c.-9C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,460,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000095 ( 0 hom. )
Consequence
RANBP17
NM_022897.5 5_prime_UTR
NM_022897.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.998
Genes affected
RANBP17 (HGNC:14428): (RAN binding protein 17) The transport of protein and large RNAs through the nuclear pore complexes (NPC) is an energy-dependent and regulated process. The import of proteins with a nuclear localization signal (NLS) is accomplished by recognition of one or more clusters of basic amino acids by the importin-alpha/beta complex; see MIM 600685 and MIM 602738. The small GTPase RAN (MIM 601179) plays a key role in NLS-dependent protein import. RAN-binding protein-17 is a member of the importin-beta superfamily of nuclear transport receptors.[supplied by OMIM, Jul 2002]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 5-170862025-C-A is Benign according to our data. Variant chr5-170862025-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041809.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP17 | NM_022897.5 | c.-9C>A | 5_prime_UTR_variant | 1/28 | ENST00000523189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP17 | ENST00000523189.6 | c.-9C>A | 5_prime_UTR_variant | 1/28 | 1 | NM_022897.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00103 AC: 156AN: 152098Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000431 AC: 3AN: 69650Hom.: 0 AF XY: 0.0000248 AC XY: 1AN XY: 40334
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GnomAD4 exome AF: 0.0000948 AC: 124AN: 1308160Hom.: 0 Cov.: 31 AF XY: 0.0000667 AC XY: 43AN XY: 644516
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GnomAD4 genome AF: 0.00101 AC: 154AN: 152206Hom.: 0 Cov.: 34 AF XY: 0.000994 AC XY: 74AN XY: 74422
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
RANBP17-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at