17-31528464-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032932.6(RAB11FIP4):c.1415T>C(p.Met472Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,510 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. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB11FIP4 | NM_032932.6 | c.1415T>C | p.Met472Thr | missense_variant | 12/15 | ENST00000621161.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB11FIP4 | ENST00000621161.5 | c.1415T>C | p.Met472Thr | missense_variant | 12/15 | 1 | NM_032932.6 | P1 | |
RAB11FIP4 | ENST00000394744.6 | c.1109T>C | p.Met370Thr | missense_variant | 10/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250952Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135676
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461288Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726912
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.1415T>C (p.M472T) alteration is located in exon 12 (coding exon 12) of the RAB11FIP4 gene. This alteration results from a T to C substitution at nucleotide position 1415, causing the methionine (M) at amino acid position 472 to be replaced by a threonine (T). 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