chr8-8319062-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080826.3(PRAG1):c.3313C>T(p.Arg1105Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,611,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R1105Q) has been classified 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.3313C>T | p.Arg1105Trp | missense_variant | 6/6 | ENST00000615670.5 | |
PRAG1 | NM_001369759.1 | c.3313C>T | p.Arg1105Trp | missense_variant | 6/6 | ||
PRAG1 | NR_163138.1 | n.3610C>T | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAG1 | ENST00000615670.5 | c.3313C>T | p.Arg1105Trp | missense_variant | 6/6 | 5 | NM_001080826.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 32AN: 241562Hom.: 0 AF XY: 0.000137 AC XY: 18AN XY: 131698
GnomAD4 exome AF: 0.000109 AC: 159AN: 1459656Hom.: 0 Cov.: 38 AF XY: 0.000118 AC XY: 86AN XY: 726222
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.3307C>T (p.R1103W) alteration is located in exon 5 (coding exon 5) of the SGK223 gene. This alteration results from a C to T substitution at nucleotide position 3307, causing the arginine (R) at amino acid position 1103 to be replaced by a tryptophan (W). 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