chr8-8318195-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080826.3(PRAG1):c.4180G>A(p.Gly1394Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,004 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 (★).
Frequency
Consequence
NM_001080826.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAG1 | NM_001080826.3 | c.4180G>A | p.Gly1394Arg | missense_variant | 6/6 | ENST00000615670.5 | |
PRAG1 | NM_001369759.1 | c.4180G>A | p.Gly1394Arg | missense_variant | 6/6 | ||
PRAG1 | NR_163138.1 | n.4477G>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAG1 | ENST00000615670.5 | c.4180G>A | p.Gly1394Arg | missense_variant | 6/6 | 5 | NM_001080826.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248254Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134894
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461716Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 727164
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.4168G>A (p.G1390R) alteration is located in exon 5 (coding exon 5) of the SGK223 gene. This alteration results from a G to A substitution at nucleotide position 4168, causing the glycine (G) at amino acid position 1390 to be replaced by an arginine (R). 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