chr8-8319037-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080826.3(PRAG1):c.3338C>A(p.Ala1113Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,612,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign 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. A1113T) has been classified as Likely benign.
Frequency
Consequence
NM_001080826.3 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 | UniProt |
---|---|---|---|---|---|---|---|
PRAG1 | NM_001080826.3 | c.3338C>A | p.Ala1113Glu | missense_variant | 6/6 | ENST00000615670.5 | |
PRAG1 | NM_001369759.1 | c.3338C>A | p.Ala1113Glu | missense_variant | 6/6 | ||
PRAG1 | NR_163138.1 | n.3635C>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAG1 | ENST00000615670.5 | c.3338C>A | p.Ala1113Glu | missense_variant | 6/6 | 5 | NM_001080826.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242854Hom.: 0 AF XY: 0.00000756 AC XY: 1AN XY: 132282
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1460824Hom.: 0 Cov.: 37 AF XY: 0.0000344 AC XY: 25AN XY: 726732
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.3332C>A (p.A1111E) alteration is located in exon 5 (coding exon 5) of the SGK223 gene. This alteration results from a C to A substitution at nucleotide position 3332, causing the alanine (A) at amino acid position 1111 to be replaced by a glutamic acid (E). 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