1-156065911-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020387.4(RAB25):āc.44T>Cā(p.Val15Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000377 in 1,590,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020387.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB25 | NM_020387.4 | c.44T>C | p.Val15Ala | missense_variant, splice_region_variant | 2/5 | ENST00000361084.10 | |
RAB25 | NR_133653.2 | n.285-2359T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB25 | ENST00000361084.10 | c.44T>C | p.Val15Ala | missense_variant, splice_region_variant | 2/5 | 1 | NM_020387.4 | P1 | |
RAB25 | ENST00000463614.1 | n.256T>C | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 2 | ||||
RAB25 | ENST00000473336.5 | n.62-2359T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
RAB25 | ENST00000487325.5 | n.239-2359T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000110 AC: 26AN: 237158Hom.: 0 AF XY: 0.000102 AC XY: 13AN XY: 127962
GnomAD4 exome AF: 0.0000375 AC: 54AN: 1438382Hom.: 0 Cov.: 31 AF XY: 0.0000337 AC XY: 24AN XY: 712724
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at