X-23785703-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002970.4(SAT1):ā€‹c.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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.46
Variant links:
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
SAT1NM_002970.4 linkuse as main transcriptc.363C>G p.Arg121= synonymous_variant 6/6 ENST00000379270.5
SAT1NR_027783.3 linkuse as main transcriptn.652C>G non_coding_transcript_exon_variant 7/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SAT1ENST00000379270.5 linkuse as main transcriptc.363C>G p.Arg121= synonymous_variant 6/61 NM_002970.4 P1

Frequencies

GnomAD3 genomes
AF:
0.000251
AC:
28
AN:
111773
Hom.:
0
Cov.:
23
AF XY:
0.000295
AC XY:
10
AN XY:
33939
show subpopulations
Gnomad AFR
AF:
0.000195
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000577
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000225
Gnomad OTH
AF:
0.00267
GnomAD3 exomes
AF:
0.000251
AC:
45
AN:
179307
Hom.:
0
AF XY:
0.000219
AC XY:
14
AN XY:
63955
show subpopulations
Gnomad AFR exome
AF:
0.000229
Gnomad AMR exome
AF:
0.000748
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000212
Gnomad OTH exome
AF:
0.00113
GnomAD4 exome
AF:
0.000253
AC:
277
AN:
1095128
Hom.:
0
Cov.:
29
AF XY:
0.000247
AC XY:
89
AN XY:
360660
show subpopulations
Gnomad4 AFR exome
AF:
0.0000759
Gnomad4 AMR exome
AF:
0.00100
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000259
Gnomad4 OTH exome
AF:
0.000435
GnomAD4 genome
AF:
0.000259
AC:
29
AN:
111828
Hom.:
0
Cov.:
23
AF XY:
0.000323
AC XY:
11
AN XY:
34004
show subpopulations
Gnomad4 AFR
AF:
0.000195
Gnomad4 AMR
AF:
0.000576
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000226
Gnomad4 OTH
AF:
0.00264
Alfa
AF:
0.000142
Hom.:
1
Bravo
AF:
0.000363

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJul 21, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
7.3
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)
0.0
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: rs142757578; hg19: chrX-23803820; API