chr8-8318806-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080826.3(PRAG1):c.3569G>A(p.Gly1190Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000129 in 1,471,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAG1 | NM_001080826.3 | c.3569G>A | p.Gly1190Asp | missense_variant | 6/6 | ENST00000615670.5 | |
PRAG1 | NM_001369759.1 | c.3569G>A | p.Gly1190Asp | missense_variant | 6/6 | ||
PRAG1 | NR_163138.1 | n.3866G>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAG1 | ENST00000615670.5 | c.3569G>A | p.Gly1190Asp | missense_variant | 6/6 | 5 | NM_001080826.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000137 AC: 2AN: 145870Hom.: 0 Cov.: 26
GnomAD4 exome AF: 0.0000121 AC: 16AN: 1325970Hom.: 0 Cov.: 40 AF XY: 0.0000155 AC XY: 10AN XY: 646278
GnomAD4 genome ? AF: 0.0000206 AC: 3AN: 145980Hom.: 0 Cov.: 26 AF XY: 0.0000141 AC XY: 1AN XY: 70990
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.3557G>A (p.G1186D) 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 3557, causing the glycine (G) at amino acid position 1186 to be replaced by an aspartic acid (D). 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