15-73884215-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153356.3(TBC1D21):c.337C>T(p.Arg113Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R113Q) has been classified as Likely benign.
Frequency
Consequence
NM_153356.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D21 | NM_153356.3 | c.337C>T | p.Arg113Trp | missense_variant | 4/11 | ENST00000300504.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D21 | ENST00000300504.7 | c.337C>T | p.Arg113Trp | missense_variant | 4/11 | 1 | NM_153356.3 | P1 | |
TBC1D21 | ENST00000535547.6 | c.229C>T | p.Arg77Trp | missense_variant | 3/10 | 1 | |||
TBC1D21 | ENST00000562056.1 | c.337C>T | p.Arg113Trp | missense_variant | 4/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251482Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135914
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727244
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.337C>T (p.R113W) alteration is located in exon 4 (coding exon 4) of the TBC1D21 gene. This alteration results from a C to T substitution at nucleotide position 337, causing the arginine (R) at amino acid position 113 to be replaced by a tryptophan (W). 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