17-31530328-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032932.6(RAB11FIP4):c.1656G>C(p.Glu552Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032932.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB11FIP4 | NM_032932.6 | c.1656G>C | p.Glu552Asp | missense_variant, splice_region_variant | 14/15 | ENST00000621161.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB11FIP4 | ENST00000621161.5 | c.1656G>C | p.Glu552Asp | missense_variant, splice_region_variant | 14/15 | 1 | NM_032932.6 | P1 | |
RAB11FIP4 | ENST00000394744.6 | c.1350G>C | p.Glu450Asp | missense_variant, splice_region_variant | 12/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251420Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135884
GnomAD4 exome AF: 0.000103 AC: 150AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.000136 AC XY: 99AN XY: 727178
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.1656G>C (p.E552D) alteration is located in exon 14 (coding exon 14) of the RAB11FIP4 gene. This alteration results from a G to C substitution at nucleotide position 1656, causing the glutamic acid (E) at amino acid position 552 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at