4-6923721-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000409757.9(TBC1D14):c.332C>T(p.Ala111Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,790 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
ENST00000409757.9 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBC1D14 | NM_020773.3 | c.332C>T | p.Ala111Val | missense_variant | 2/14 | ENST00000409757.9 | NP_065824.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D14 | ENST00000409757.9 | c.332C>T | p.Ala111Val | missense_variant | 2/14 | 1 | NM_020773.3 | ENSP00000386921 | ||
TBC1D14 | ENST00000448507.5 | c.332C>T | p.Ala111Val | missense_variant | 2/14 | 5 | ENSP00000404041 | |||
TBC1D14 | ENST00000444368.1 | c.332C>T | p.Ala111Val | missense_variant | 2/2 | 3 | ENSP00000414951 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251026Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135778
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461526Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727088
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.332C>T (p.A111V) alteration is located in exon 2 (coding exon 1) of the TBC1D14 gene. This alteration results from a C to T substitution at nucleotide position 332, causing the alanine (A) at amino acid position 111 to be replaced by a valine (V). 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