chr10-51153227-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006258.4(PRKG1):c.375G>A(p.Ser125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,612,338 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S125S) has been classified as Likely benign.
Frequency
Consequence
NM_006258.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKG1 | NM_006258.4 | c.375G>A | p.Ser125= | synonymous_variant | 2/18 | ENST00000373980.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKG1 | ENST00000373980.11 | c.375G>A | p.Ser125= | synonymous_variant | 2/18 | 1 | NM_006258.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 151886Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250868Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135600
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1460452Hom.: 0 Cov.: 30 AF XY: 0.0000440 AC XY: 32AN XY: 726552
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 151886Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74186
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2022 | 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. - |
Aortic aneurysm, familial thoracic 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at