2-88691844-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_144563.3(RPIA):c.146C>T(p.Ser49Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,598,334 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144563.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPIA | NM_144563.3 | c.146C>T | p.Ser49Phe | missense_variant | 1/9 | ENST00000283646.5 | |
RPIA | XM_047443733.1 | c.146C>T | p.Ser49Phe | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPIA | ENST00000283646.5 | c.146C>T | p.Ser49Phe | missense_variant | 1/9 | 1 | NM_144563.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000988 AC: 15AN: 151896Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000237 AC: 5AN: 211378Hom.: 0 AF XY: 0.0000259 AC XY: 3AN XY: 116032
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1446438Hom.: 0 Cov.: 32 AF XY: 0.00000696 AC XY: 5AN XY: 718284
GnomAD4 genome ? AF: 0.0000988 AC: 15AN: 151896Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5AN XY: 74204
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.146C>T (p.S49F) alteration is located in exon 1 (coding exon 1) of the RPIA gene. This alteration results from a C to T substitution at nucleotide position 146, causing the serine (S) at amino acid position 49 to be replaced by a phenylalanine (F). 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