3-128726387-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004637.6(RAB7A):c.-9+28G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 152,070 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RAB7A
NM_004637.6 intron
NM_004637.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0600
Genes affected
RAB7A (HGNC:9788): (RAB7A, member RAS oncogene family) RAB family members are small, RAS-related GTP-binding proteins that are important regulators of vesicular transport. Each RAB protein targets multiple proteins that act in exocytic / endocytic pathways. This gene encodes a RAB family member that regulates vesicle traffic in the late endosomes and also from late endosomes to lysosomes. This encoded protein is also involved in the cellular vacuolation of the VacA cytotoxin of Helicobacter pylori. Mutations at highly conserved amino acid residues in this gene have caused some forms of Charcot-Marie-Tooth (CMT) type 2 neuropathies. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 3-128726387-G-T is Benign according to our data. Variant chr3-128726387-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1683833.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 502 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB7A | NM_004637.6 | c.-9+28G>T | intron_variant | ENST00000265062.8 | NP_004628.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB7A | ENST00000265062.8 | c.-9+28G>T | intron_variant | 1 | NM_004637.6 | ENSP00000265062.3 |
Frequencies
GnomAD3 genomes AF: 0.00329 AC: 500AN: 151962Hom.: 4 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 332Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 232
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GnomAD4 genome AF: 0.00330 AC: 502AN: 152070Hom.: 4 Cov.: 32 AF XY: 0.00301 AC XY: 224AN XY: 74350
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2021 | See Variant Classification Assertion Criteria. - |
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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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