16-2475183-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001199107.2(TBC1D24):c.-116+13G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000336 in 148,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001199107.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBC1D24 | NM_001199107.2 | c.-116+13G>C | intron_variant | Intron 1 of 7 | ENST00000646147.1 | NP_001186036.1 | ||
TBC1D24 | NM_020705.3 | c.-116+13G>C | intron_variant | Intron 1 of 6 | NP_065756.1 | |||
TBC1D24 | XM_017023493.2 | c.-116+13G>C | intron_variant | Intron 1 of 8 | XP_016878982.1 | |||
TBC1D24 | XM_017023495.2 | c.-116+13G>C | intron_variant | Intron 1 of 7 | XP_016878984.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D24 | ENST00000646147.1 | c.-116+13G>C | intron_variant | Intron 1 of 7 | NM_001199107.2 | ENSP00000494678.1 | ||||
TBC1D24 | ENST00000567020.6 | c.-116+13G>C | intron_variant | Intron 1 of 6 | 1 | ENSP00000454408.1 | ||||
TBC1D24 | ENST00000569874.2 | n.-116+13G>C | intron_variant | Intron 1 of 7 | 5 | ENSP00000455005.2 | ||||
TBC1D24 | ENST00000630263.2 | n.-142+13G>C | intron_variant | Intron 1 of 7 | 5 | ENSP00000486835.1 |
Frequencies
GnomAD3 genomes AF: 0.0000336 AC: 5AN: 148818Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 686Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 330
GnomAD4 genome AF: 0.0000336 AC: 5AN: 148818Hom.: 0 Cov.: 33 AF XY: 0.0000414 AC XY: 3AN XY: 72506
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at