8-8319134-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080826.3(PRAG1):c.3241C>T(p.Pro1081Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,605,640 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAG1 | NM_001080826.3 | c.3241C>T | p.Pro1081Ser | missense_variant | 6/6 | ENST00000615670.5 | |
PRAG1 | NM_001369759.1 | c.3241C>T | p.Pro1081Ser | missense_variant | 6/6 | ||
PRAG1 | NR_163138.1 | n.3538C>T | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAG1 | ENST00000615670.5 | c.3241C>T | p.Pro1081Ser | missense_variant | 6/6 | 5 | NM_001080826.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000300 AC: 71AN: 236606Hom.: 0 AF XY: 0.000310 AC XY: 40AN XY: 128972
GnomAD4 exome AF: 0.000183 AC: 266AN: 1453332Hom.: 0 Cov.: 38 AF XY: 0.000197 AC XY: 142AN XY: 722452
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 27, 2022 | The c.3235C>T (p.P1079S) 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 3235, causing the proline (P) at amino acid position 1079 to be replaced by a serine (S). 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