chr15-73887666-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_153356.3(TBC1D21):c.824C>T(p.Ala275Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,086 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D21 | ENST00000300504.7 | c.824C>T | p.Ala275Val | missense_variant | Exon 9 of 11 | 1 | NM_153356.3 | ENSP00000300504.2 | ||
TBC1D21 | ENST00000535547.6 | c.716C>T | p.Ala239Val | missense_variant | Exon 8 of 10 | 1 | ENSP00000439325.2 | |||
TBC1D21 | ENST00000562056.1 | c.713C>T | p.Ala238Val | missense_variant | Exon 8 of 10 | 5 | ENSP00000457096.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 250876Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135644
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461752Hom.: 2 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727176
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.824C>T (p.A275V) alteration is located in exon 9 (coding exon 9) of the TBC1D21 gene. This alteration results from a C to T substitution at nucleotide position 824, causing the alanine (A) at amino acid position 275 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