X-23785703-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002970.4(SAT1):āc.363C>Gā(p.Arg121=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000254 in 1,206,956 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 100 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00026 ( 0 hom., 11 hem., cov: 23)
Exomes š: 0.00025 ( 0 hom. 89 hem. )
Consequence
SAT1
NM_002970.4 synonymous
NM_002970.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.46
Genes affected
SAT1 (HGNC:10540): (spermidine/spermine N1-acetyltransferase 1) The protein encoded by this gene belongs to the acetyltransferase family, and is a rate-limiting enzyme in the catabolic pathway of polyamine metabolism. It catalyzes the acetylation of spermidine and spermine, and is involved in the regulation of the intracellular concentration of polyamines and their transport out of cells. Defects in this gene are associated with keratosis follicularis spinulosa decalvans (KFSD). Alternatively spliced transcripts have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant X-23785703-C-G is Benign according to our data. Variant chrX-23785703-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 713838.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.46 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 11 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAT1 | NM_002970.4 | c.363C>G | p.Arg121= | synonymous_variant | 6/6 | ENST00000379270.5 | |
SAT1 | NR_027783.3 | n.652C>G | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAT1 | ENST00000379270.5 | c.363C>G | p.Arg121= | synonymous_variant | 6/6 | 1 | NM_002970.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000251 AC: 28AN: 111773Hom.: 0 Cov.: 23 AF XY: 0.000295 AC XY: 10AN XY: 33939
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GnomAD3 exomes AF: 0.000251 AC: 45AN: 179307Hom.: 0 AF XY: 0.000219 AC XY: 14AN XY: 63955
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GnomAD4 exome AF: 0.000253 AC: 277AN: 1095128Hom.: 0 Cov.: 29 AF XY: 0.000247 AC XY: 89AN XY: 360660
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GnomAD4 genome AF: 0.000259 AC: 29AN: 111828Hom.: 0 Cov.: 23 AF XY: 0.000323 AC XY: 11AN XY: 34004
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at