chr1-205770811-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003929.3(RAB29):c.422G>A(p.Arg141Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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. R141G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003929.3 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 | UniProt |
---|---|---|---|---|---|---|---|
RAB29 | NM_003929.3 | c.422G>A | p.Arg141Gln | missense_variant | 5/6 | ENST00000367139.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB29 | ENST00000367139.8 | c.422G>A | p.Arg141Gln | missense_variant | 5/6 | 1 | NM_003929.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251444Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135896
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727224
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 05, 2024 | The c.422G>A (p.R141Q) alteration is located in exon 5 (coding exon 4) of the RAB29 gene. This alteration results from a G to A substitution at nucleotide position 422, causing the arginine (R) at amino acid position 141 to be replaced by a glutamine (Q). 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