8-37871396-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001002814.3(RAB11FIP1):c.3406G>A(p.Ala1136Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000065 in 1,614,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001002814.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB11FIP1 | NM_001002814.3 | c.3406G>A | p.Ala1136Thr | missense_variant | Exon 4 of 6 | ENST00000330843.9 | NP_001002814.2 | |
RAB11FIP1 | XM_017013869.2 | c.3406G>A | p.Ala1136Thr | missense_variant | Exon 4 of 4 | XP_016869358.1 | ||
RAB11FIP1 | NM_025151.5 | c.1623-868G>A | intron_variant | Intron 3 of 4 | NP_079427.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251462Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135902
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 727248
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3406G>A (p.A1136T) alteration is located in exon 4 (coding exon 4) of the RAB11FIP1 gene. This alteration results from a G to A substitution at nucleotide position 3406, causing the alanine (A) at amino acid position 1136 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