rs7627396
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_004162.5(RAB5A):c.163+10475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 152,354 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.012 ( 22 hom., cov: 33)
Consequence
RAB5A
NM_004162.5 intron
NM_004162.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.10
Genes affected
RAB5A (HGNC:9783): (RAB5A, member RAS oncogene family) Enables GDP binding activity; GTP binding activity; and GTPase activity. Involved in several processes, including amyloid-beta clearance by transcytosis; early endosome to late endosome transport; and regulation of exocytosis. Located in several cellular components, including cytoplasmic side of early endosome membrane; nucleoplasm; and terminal bouton. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0119 (1809/152354) while in subpopulation NFE AF= 0.0158 (1075/68040). AF 95% confidence interval is 0.015. There are 22 homozygotes in gnomad4. There are 834 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1809 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB5A | NM_004162.5 | c.163+10475A>G | intron_variant | ENST00000273047.9 | |||
RAB5A | NM_001292048.2 | c.163+10475A>G | intron_variant | ||||
RAB5A | XM_047448648.1 | c.-268-9012A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB5A | ENST00000273047.9 | c.163+10475A>G | intron_variant | 1 | NM_004162.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0119 AC: 1811AN: 152236Hom.: 23 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0119 AC: 1809AN: 152354Hom.: 22 Cov.: 33 AF XY: 0.0112 AC XY: 834AN XY: 74516
GnomAD4 genome
?
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1809
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33
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834
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74516
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21
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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