chr17-31434082-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032932.6(RAB11FIP4):c.296C>T(p.Thr99Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000151 in 1,585,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032932.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB11FIP4 | ENST00000621161.5 | c.296C>T | p.Thr99Met | missense_variant | Exon 3 of 15 | 1 | NM_032932.6 | ENSP00000482620.1 | ||
RAB11FIP4 | ENST00000582009.5 | c.164C>T | p.Thr55Met | missense_variant | Exon 3 of 5 | 3 | ENSP00000463206.1 | |||
RAB11FIP4 | ENST00000579908.1 | n.137C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151882Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000142 AC: 3AN: 211064Hom.: 0 AF XY: 0.0000176 AC XY: 2AN XY: 113744
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1433940Hom.: 0 Cov.: 31 AF XY: 0.0000183 AC XY: 13AN XY: 711686
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.296C>T (p.T99M) alteration is located in exon 3 (coding exon 3) of the RAB11FIP4 gene. This alteration results from a C to T substitution at nucleotide position 296, causing the threonine (T) at amino acid position 99 to be replaced by a methionine (M). 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