19-43258351-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002784.5(PSG9):āc.1094T>Cā(p.Phe365Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,592,864 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002784.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSG9 | NM_002784.5 | c.1094T>C | p.Phe365Ser | missense_variant | 5/6 | ENST00000270077.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSG9 | ENST00000270077.8 | c.1094T>C | p.Phe365Ser | missense_variant | 5/6 | 1 | NM_002784.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000341 AC: 5AN: 146720Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000568 AC: 14AN: 246458Hom.: 1 AF XY: 0.0000824 AC XY: 11AN XY: 133552
GnomAD4 exome AF: 0.0000325 AC: 47AN: 1446144Hom.: 2 Cov.: 33 AF XY: 0.0000361 AC XY: 26AN XY: 719624
GnomAD4 genome AF: 0.0000341 AC: 5AN: 146720Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 71564
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at