4-98343186-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001100427.2(RAP1GDS1):āc.160T>Cā(p.Phe54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,607,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001100427.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAP1GDS1 | NM_001100427.2 | c.160T>C | p.Phe54Leu | missense_variant | 3/15 | ENST00000408927.8 | NP_001093897.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAP1GDS1 | ENST00000408927.8 | c.160T>C | p.Phe54Leu | missense_variant | 3/15 | 2 | NM_001100427.2 | ENSP00000386153 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249042Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135142
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1455244Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 724406
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 27, 2023 | The c.163T>C (p.F55L) alteration is located in exon 3 (coding exon 3) of the RAP1GDS1 gene. This alteration results from a T to C substitution at nucleotide position 163, causing the phenylalanine (F) at amino acid position 55 to be replaced by a leucine (L). 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