16-30358156-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015527.4(TBC1D10B):c.2215G>A(p.Glu739Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,549,546 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E739G) has been classified as Uncertain significance.
Frequency
Consequence
NM_015527.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151930Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000633 AC: 1AN: 157958Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82798
GnomAD4 exome AF: 0.000143 AC: 200AN: 1397616Hom.: 0 Cov.: 31 AF XY: 0.000136 AC XY: 94AN XY: 689258
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151930Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2215G>A (p.E739K) alteration is located in exon 9 (coding exon 9) of the TBC1D10B gene. This alteration results from a G to A substitution at nucleotide position 2215, causing the glutamic acid (E) at amino acid position 739 to be replaced by a lysine (K). 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