16-2475148-TGAG-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001199107.2(TBC1D24):c.-134_-132delGAG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00006 in 149,928 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001199107.2 5_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|
TBC1D24 | NM_001199107.2 | c.-134_-132delGAG | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000646147.1 | NP_001186036.1 | ||
TBC1D24 | NM_020705.3 | c.-134_-132delGAG | 5_prime_UTR_variant | Exon 1 of 7 | NP_065756.1 | |||
TBC1D24 | XM_017023493.2 | c.-134_-132delGAG | 5_prime_UTR_variant | Exon 1 of 9 | XP_016878982.1 | |||
TBC1D24 | XM_017023495.2 | c.-134_-132delGAG | 5_prime_UTR_variant | Exon 1 of 8 | XP_016878984.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000601 AC: 9AN: 149822Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 444Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 210
GnomAD4 genome AF: 0.0000600 AC: 9AN: 149928Hom.: 0 Cov.: 33 AF XY: 0.0000410 AC XY: 3AN XY: 73230
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