rs858520
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_133491.5(SAT2):c.294G>A(p.Pro98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,612,372 control chromosomes in the GnomAD database, including 111,451 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.29 ( 7874 hom., cov: 31)
Exomes 𝑓: 0.37 ( 103577 hom. )
Consequence
SAT2
NM_133491.5 synonymous
NM_133491.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -6.25
Genes affected
SAT2 (HGNC:23160): (spermidine/spermine N1-acetyltransferase family member 2) Enables diamine N-acetyltransferase activity and identical protein binding activity. Involved in polyamine metabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
SHBG (HGNC:10839): (sex hormone binding globulin) This gene encodes a steroid binding protein that was first described as a plasma protein secreted by the liver but is now thought to participate in the regulation of steroid responses. The encoded protein transports androgens and estrogens in the blood, binding each steroid molecule as a dimer formed from identical or nearly identical monomers. Polymorphisms in this gene have been associated with polycystic ovary syndrome and type 2 diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP7
Synonymous conserved (PhyloP=-6.25 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAT2 | NM_133491.5 | c.294G>A | p.Pro98= | synonymous_variant | 4/6 | ENST00000269298.10 | NP_597998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAT2 | ENST00000269298.10 | c.294G>A | p.Pro98= | synonymous_variant | 4/6 | 1 | NM_133491.5 | ENSP00000269298 | P1 |
Frequencies
GnomAD3 genomes AF: 0.290 AC: 43985AN: 151818Hom.: 7873 Cov.: 31
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GnomAD3 exomes AF: 0.352 AC: 88422AN: 251072Hom.: 16962 AF XY: 0.371 AC XY: 50318AN XY: 135804
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GnomAD4 exome AF: 0.370 AC: 540658AN: 1460436Hom.: 103577 Cov.: 34 AF XY: 0.376 AC XY: 273352AN XY: 726638
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GnomAD4 genome AF: 0.290 AC: 43987AN: 151936Hom.: 7874 Cov.: 31 AF XY: 0.294 AC XY: 21825AN XY: 74238
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at