rs858520

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.25
Variant links:
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
SAT2NM_133491.5 linkuse as main transcriptc.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
SAT2ENST00000269298.10 linkuse as main transcriptc.294G>A p.Pro98= synonymous_variant 4/61 NM_133491.5 ENSP00000269298 P1

Frequencies

GnomAD3 genomes
AF:
0.290
AC:
43985
AN:
151818
Hom.:
7873
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0762
Gnomad AMI
AF:
0.372
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.437
Gnomad EAS
AF:
0.282
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.378
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.384
Gnomad OTH
AF:
0.330
GnomAD3 exomes
AF:
0.352
AC:
88422
AN:
251072
Hom.:
16962
AF XY:
0.371
AC XY:
50318
AN XY:
135804
show subpopulations
Gnomad AFR exome
AF:
0.0662
Gnomad AMR exome
AF:
0.257
Gnomad ASJ exome
AF:
0.438
Gnomad EAS exome
AF:
0.280
Gnomad SAS exome
AF:
0.476
Gnomad FIN exome
AF:
0.367
Gnomad NFE exome
AF:
0.388
Gnomad OTH exome
AF:
0.390
GnomAD4 exome
AF:
0.370
AC:
540658
AN:
1460436
Hom.:
103577
Cov.:
34
AF XY:
0.376
AC XY:
273352
AN XY:
726638
show subpopulations
Gnomad4 AFR exome
AF:
0.0622
Gnomad4 AMR exome
AF:
0.266
Gnomad4 ASJ exome
AF:
0.436
Gnomad4 EAS exome
AF:
0.266
Gnomad4 SAS exome
AF:
0.477
Gnomad4 FIN exome
AF:
0.365
Gnomad4 NFE exome
AF:
0.377
Gnomad4 OTH exome
AF:
0.365
GnomAD4 genome
AF:
0.290
AC:
43987
AN:
151936
Hom.:
7874
Cov.:
31
AF XY:
0.294
AC XY:
21825
AN XY:
74238
show subpopulations
Gnomad4 AFR
AF:
0.0761
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.437
Gnomad4 EAS
AF:
0.282
Gnomad4 SAS
AF:
0.468
Gnomad4 FIN
AF:
0.378
Gnomad4 NFE
AF:
0.384
Gnomad4 OTH
AF:
0.328
Alfa
AF:
0.374
Hom.:
21680
Bravo
AF:
0.268
Asia WGS
AF:
0.332
AC:
1154
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
7.0
DANN
Benign
0.79
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.18
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs858520; hg19: chr17-7530271; COSMIC: COSV52646326; COSMIC: COSV52646326; API