chr19-47197285-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005500.3(SAE1):c.786T>C(p.Tyr262=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,614,022 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 5 hom., cov: 31)
Exomes 𝑓: 0.0045 ( 52 hom. )
Consequence
SAE1
NM_005500.3 synonymous
NM_005500.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.38
Genes affected
SAE1 (HGNC:30660): (SUMO1 activating enzyme subunit 1) Posttranslational modification of proteins by the addition of the small protein SUMO (see SUMO1; MIM 601912), or sumoylation, regulates protein structure and intracellular localization. SAE1 and UBA2 (MIM 613295) form a heterodimer that functions as a SUMO-activating enzyme for the sumoylation of proteins (Okuma et al., 1999 [PubMed 9920803]).[supplied by OMIM, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 19-47197285-T-C is Benign according to our data. Variant chr19-47197285-T-C is described in ClinVar as [Benign]. Clinvar id is 778848.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00285 (434/152276) while in subpopulation SAS AF= 0.0249 (120/4828). AF 95% confidence interval is 0.0212. There are 5 homozygotes in gnomad4. There are 237 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAE1 | NM_005500.3 | c.786T>C | p.Tyr262= | synonymous_variant | 7/9 | ENST00000270225.12 | |
SAE1 | NM_001145713.2 | c.734-11874T>C | intron_variant | ||||
SAE1 | NM_001145714.2 | c.734-6386T>C | intron_variant | ||||
SAE1 | NR_027280.2 | n.966T>C | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAE1 | ENST00000270225.12 | c.786T>C | p.Tyr262= | synonymous_variant | 7/9 | 1 | NM_005500.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00285 AC: 433AN: 152158Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.00489 AC: 1230AN: 251464Hom.: 10 AF XY: 0.00606 AC XY: 824AN XY: 135908
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GnomAD4 exome AF: 0.00448 AC: 6548AN: 1461746Hom.: 52 Cov.: 32 AF XY: 0.00511 AC XY: 3713AN XY: 727186
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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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