17-31528522-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_032932.6(RAB11FIP4):c.1473G>T(p.Lys491Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,613,764 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
RAB11FIP4
NM_032932.6 missense
NM_032932.6 missense
Scores
1
10
5
Clinical Significance
Conservation
PhyloP100: 2.50
Genes affected
RAB11FIP4 (HGNC:30267): (RAB11 family interacting protein 4) The protein encoded by this gene interacts with RAB11 and is thought to be involved in bringing recycling endosome membranes to the cleavage furrow in late cytokinesis. Hypoxic conditions can lead to an upregulation of the encoded protein and enhance the metastatic potential of hepatocellular carcinoma. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB11FIP4 | NM_032932.6 | c.1473G>T | p.Lys491Asn | missense_variant | 12/15 | ENST00000621161.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB11FIP4 | ENST00000621161.5 | c.1473G>T | p.Lys491Asn | missense_variant | 12/15 | 1 | NM_032932.6 | P1 | |
RAB11FIP4 | ENST00000394744.6 | c.1167G>T | p.Lys389Asn | missense_variant | 10/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152258Hom.: 0 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251100Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135754
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GnomAD4 exome AF: 0.000196 AC: 287AN: 1461506Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 727042
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GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74388
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | The c.1473G>T (p.K491N) alteration is located in exon 12 (coding exon 12) of the RAB11FIP4 gene. This alteration results from a G to T substitution at nucleotide position 1473, causing the lysine (K) at amino acid position 491 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Loss of ubiquitination at K491 (P = 0.003);.;
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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