19-5924882-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007322.3(RANBP3):c.941C>T(p.Ala314Val) variant causes a missense change. The variant allele was found at a frequency of 0.00396 in 1,614,092 control chromosomes in the GnomAD database, including 198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.020 ( 109 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 89 hom. )
Consequence
RANBP3
NM_007322.3 missense
NM_007322.3 missense
Scores
1
4
11
Clinical Significance
Conservation
PhyloP100: 5.71
Genes affected
RANBP3 (HGNC:9850): (RAN binding protein 3) This gene encodes a protein with a RanBD1 domain that is found in both the nucleus and cytoplasm. This protein plays a role in nuclear export as part of a heteromeric complex. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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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=0.0018642545).
BP6
?
Variant 19-5924882-G-A is Benign according to our data. Variant chr19-5924882-G-A is described in ClinVar as [Benign]. Clinvar id is 773081.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP3 | NM_007322.3 | c.941C>T | p.Ala314Val | missense_variant | 11/17 | ENST00000340578.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP3 | ENST00000340578.10 | c.941C>T | p.Ala314Val | missense_variant | 11/17 | 1 | NM_007322.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0200 AC: 3044AN: 152204Hom.: 109 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00543 AC: 1354AN: 249584Hom.: 33 AF XY: 0.00393 AC XY: 532AN XY: 135406
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GnomAD4 exome AF: 0.00228 AC: 3339AN: 1461770Hom.: 89 Cov.: 30 AF XY: 0.00200 AC XY: 1458AN XY: 727206
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GnomAD4 genome ? AF: 0.0200 AC: 3054AN: 152322Hom.: 109 Cov.: 33 AF XY: 0.0195 AC XY: 1453AN XY: 74492
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ESP6500AA
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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 | May 21, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;.;N;.;.
REVEL
Benign
Sift
Uncertain
D;D;.;T;.;.
Sift4G
Benign
T;T;T;T;T;D
Polyphen
P;B;P;P;.;.
Vest4
MVP
MPC
0.54
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