17-78403907-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024419.5(PGS1):c.1220A>G(p.Gln407Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024419.5 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 |
---|---|---|---|---|---|---|---|
PGS1 | NM_024419.5 | c.1220A>G | p.Gln407Arg | missense_variant | 7/10 | ENST00000262764.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGS1 | ENST00000262764.11 | c.1220A>G | p.Gln407Arg | missense_variant | 7/10 | 1 | NM_024419.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249488Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135354
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461820Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 727200
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.1220A>G (p.Q407R) alteration is located in exon 7 (coding exon 7) of the PGS1 gene. This alteration results from a A to G substitution at nucleotide position 1220, causing the glutamine (Q) at amino acid position 407 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