rs5626
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000961.4(PTGIS):c.706C>T(p.Arg236Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 1,614,158 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R236L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGIS | NM_000961.4 | c.706C>T | p.Arg236Cys | missense_variant | 6/10 | ENST00000244043.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGIS | ENST00000244043.5 | c.706C>T | p.Arg236Cys | missense_variant | 6/10 | 1 | NM_000961.4 | P1 | |
PTGIS | ENST00000478971.1 | n.527C>T | non_coding_transcript_exon_variant | 5/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00783 AC: 1192AN: 152186Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00197 AC: 496AN: 251358Hom.: 2 AF XY: 0.00141 AC XY: 192AN XY: 135862
GnomAD4 exome AF: 0.000830 AC: 1213AN: 1461854Hom.: 9 Cov.: 33 AF XY: 0.000696 AC XY: 506AN XY: 727226
GnomAD4 genome ? AF: 0.00783 AC: 1193AN: 152304Hom.: 14 Cov.: 32 AF XY: 0.00732 AC XY: 545AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at