Genetic Variant SAT1:c.202+7C>G (chrX-23783890-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002970.4(SAT1):c.202+7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 23)

Consequence

SAT1
NM_002970.4 splice_region, intron

Scores

Splicing: ADA: 0.0002713

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.498

Publications

0 publications found

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]

SAT1 Gene-Disease associations (from GenCC):

systemic lupus erythematosus
Inheritance: XL Classification: STRONG Submitted by: PanelApp Australia
pediatric systemic lupus erythematosus
Inheritance: XL Classification: LIMITED Submitted by: ClinGen

SAT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.064358294).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002970.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAT1	NM_002970.4	MANE Select	c.202+7C>G		splice_region intron	N/A	NP_002961.1	P21673
	SAT1	NR_027783.3		n.381+7C>G		splice_region intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SAT1	ENST00000379270.5	TSL:1 MANE Select	c.202+7C>G	splice_region intron	N/A	ENSP00000368572.4	P21673
SAT1	ENST00000379254.5	TSL:3	c.118+181C>G	intron	N/A	ENSP00000368556.1	E9PD37
SAT1	ENST00000379251.7	TSL:2	n.478C>G	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000545

AC:

AN:

183418

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000122

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.94

CADD

Benign

9.0

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0055

FATHMM_MKL

Benign

0.079

LIST_S2

Benign

0.36

M_CAP

Benign

0.081

MetaRNN

Benign

0.064

MetaSVM

Benign

-1.0

PhyloP100

-0.50

PROVEAN

Benign

-0.18

REVEL

Benign

0.058

Sift

Uncertain

0.0030

Sift4G

Pathogenic

0.0

Polyphen

0.0010

Vest4

0.19

MutPred

0.10

Loss of glycosylation at P70 (P = 0.052)

MVP

0.12

ClinPred

0.047

GERP RS

-0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00027

dbscSNV1_RF

Benign

0.038

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over