X-23783476-A-G

Position:

• chrX-23783476-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_002970.4(SAT1):​c.66+59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.72 (20457 hom., 22856 hem., cov: 22)
  • Exomes 𝑓: 0.78 (210336 hom. 230774 hem.)
  • Failed GnomAD Quality Control
• Consequence: SAT1 NM_002970.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAT1	NM_002970.4	c.66+59A>G		intron_variant		ENST00000379270.5	NP_002961.1
SAT1	NR_027783.3	n.245+59A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAT1	ENST00000379270.5	c.66+59A>G		intron_variant		1	NM_002970.4	ENSP00000368572.4

Frequencies

GnomAD3 genomes AF: 0.719 AC: 78839 AN: 109630 Hom.: 20451 Cov.: 22 AF XY: 0.715 AC XY: 22804 AN XY: 31904

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.717

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.784 AC: 769920 AN: 981905 Hom.: 210336 Cov.: 16 AF XY: 0.806 AC XY: 230774 AN XY: 286151

Gnomad4 AFR exome AF: 0.623

Gnomad4 AMR exome AF: 0.555

Gnomad4 ASJ exome AF: 0.768

Gnomad4 EAS exome AF: 0.641

Gnomad4 SAS exome AF: 0.837

Gnomad4 FIN exome AF: 0.777

Gnomad4 NFE exome AF: 0.803

Gnomad4 OTH exome AF: 0.765

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.719 AC: 78895 AN: 109680 Hom.: 20457 Cov.: 22 AF XY: 0.715 AC XY: 22856 AN XY: 31964

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.722

Alfa AF: 0.768 Hom.: 40956

Bravo AF: 0.698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs3764885; hg19: chrX-23801593; COSMIC: COSV63380763; COSMIC: COSV63380763;