rs922834
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_198490.3(RAB43):c.205-12263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00714 in 152,004 control chromosomes in the GnomAD database, including 8 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 0.0071 ( 8 hom., cov: 32)
Consequence
RAB43
NM_198490.3 intron
NM_198490.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.51
Genes affected
RAB43 (HGNC:19983): (RAB43, member RAS oncogene family) Enables GTPase activity. Involved in several processes, including Golgi organization; phagosome maturation; and retrograde transport, plasma membrane to Golgi. Located in Golgi apparatus and phagocytic vesicle. [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=-0.97).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00714 (1085/152004) while in subpopulation AFR AF= 0.0197 (818/41446). AF 95% confidence interval is 0.0186. There are 8 homozygotes in gnomad4. There are 508 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB43 | NM_198490.3 | c.205-12263C>T | intron_variant | ENST00000315150.10 | |||
ISY1-RAB43 | NM_001204890.2 | c.852-12263C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB43 | ENST00000315150.10 | c.205-12263C>T | intron_variant | 1 | NM_198490.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00706 AC: 1073AN: 151886Hom.: 8 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00714 AC: 1085AN: 152004Hom.: 8 Cov.: 32 AF XY: 0.00684 AC XY: 508AN XY: 74312
GnomAD4 genome
?
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152004
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32
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508
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74312
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12
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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