chr3-129094987-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_198490.3(RAB43):c.387C>T(p.Ile129=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,610,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198490.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB43 | NM_198490.3 | c.387C>T | p.Ile129= | splice_region_variant, synonymous_variant | 2/3 | ENST00000315150.10 | |
ISY1-RAB43 | NM_001204890.2 | c.*38C>T | splice_region_variant, 3_prime_UTR_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB43 | ENST00000315150.10 | c.387C>T | p.Ile129= | splice_region_variant, synonymous_variant | 2/3 | 1 | NM_198490.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152046Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248574Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134402
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1458404Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 725346
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152046Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74240
ClinVar
Submissions by phenotype
RAB43-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 23, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at