4-98379116-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001100427.2(RAP1GDS1):c.461T>C(p.Leu154Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,457,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L154F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001100427.2 missense
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 |
---|---|---|---|---|---|---|---|
RAP1GDS1 | NM_001100427.2 | c.461T>C | p.Leu154Pro | missense_variant | 5/15 | ENST00000408927.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAP1GDS1 | ENST00000408927.8 | c.461T>C | p.Leu154Pro | missense_variant | 5/15 | 2 | NM_001100427.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246300Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133688
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457812Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 725118
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.464T>C (p.L155P) alteration is located in exon 5 (coding exon 5) of the RAP1GDS1 gene. This alteration results from a T to C substitution at nucleotide position 464, causing the leucine (L) at amino acid position 155 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at