chr1-205771540-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003929.3(RAB29):c.310C>G(p.Gln104Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0146 in 1,614,136 control chromosomes in the GnomAD database, including 256 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0098 ( 13 hom., cov: 32)
Exomes 𝑓: 0.015 ( 243 hom. )
Consequence
RAB29
NM_003929.3 missense
NM_003929.3 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 5.02
Genes affected
RAB29 (HGNC:9789): (RAB29, member RAS oncogene family) Enables several functions, including dynein complex binding activity; guanyl ribonucleotide binding activity; and kinesin binding activity. Involved in several processes, including positive regulation of T cell receptor signaling pathway; positive regulation of receptor recycling; and toxin transport. Located in several cellular components, including Golgi apparatus; endosome; and vacuole. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.007671267).
BP6
?
Variant 1-205771540-G-C is Benign according to our data. Variant chr1-205771540-G-C is described in ClinVar as [Benign]. Clinvar id is 3037484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-205771540-G-C is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00979 (1491/152288) while in subpopulation SAS AF= 0.0249 (120/4822). AF 95% confidence interval is 0.0213. There are 13 homozygotes in gnomad4. There are 748 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB29 | NM_003929.3 | c.310C>G | p.Gln104Glu | missense_variant | 4/6 | ENST00000367139.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB29 | ENST00000367139.8 | c.310C>G | p.Gln104Glu | missense_variant | 4/6 | 1 | NM_003929.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00982 AC: 1494AN: 152170Hom.: 13 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0125 AC: 3142AN: 251490Hom.: 39 AF XY: 0.0140 AC XY: 1897AN XY: 135920
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GnomAD4 exome AF: 0.0151 AC: 22117AN: 1461848Hom.: 243 Cov.: 32 AF XY: 0.0157 AC XY: 11429AN XY: 727228
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GnomAD4 genome ? AF: 0.00979 AC: 1491AN: 152288Hom.: 13 Cov.: 32 AF XY: 0.0100 AC XY: 748AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RAB29-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;.;N
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;.;B
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at