22-46797588-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014346.5(TBC1D22A):āc.605A>Gā(p.Lys202Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,610,904 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 (ā ).
Frequency
Consequence
NM_014346.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248468Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134770
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1458542Hom.: 0 Cov.: 31 AF XY: 0.0000290 AC XY: 21AN XY: 725024
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.605A>G (p.K202R) alteration is located in exon 4 (coding exon 4) of the TBC1D22A gene. This alteration results from a A to G substitution at nucleotide position 605, causing the lysine (K) at amino acid position 202 to be replaced by an arginine (R). 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