15-69455180-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001003.3(RPLP1):āc.158A>Gā(p.Asn53Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000503 in 1,591,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N53K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001003.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPLP1 | NM_001003.3 | c.158A>G | p.Asn53Ser | missense_variant | 3/4 | ENST00000260379.11 | |
RPLP1 | NM_213725.2 | c.83A>G | p.Asn28Ser | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPLP1 | ENST00000260379.11 | c.158A>G | p.Asn53Ser | missense_variant | 3/4 | 1 | NM_001003.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000213 AC: 5AN: 234312Hom.: 0 AF XY: 0.0000315 AC XY: 4AN XY: 126854
GnomAD4 exome AF: 0.0000528 AC: 76AN: 1439728Hom.: 0 Cov.: 30 AF XY: 0.0000503 AC XY: 36AN XY: 715158
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 09, 2022 | The c.158A>G (p.N53S) alteration is located in exon 3 (coding exon 3) of the RPLP1 gene. This alteration results from a A to G substitution at nucleotide position 158, causing the asparagine (N) at amino acid position 53 to be replaced by a serine (S). 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