rs11550721

chrX-23783194-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002970.4(SAT1):c.-158C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 492,990 control chromosomes in the GnomAD database, including 8,542 homozygotes. There are 30,372 hemizygotes in GnomAD. 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 0.17 (1592 hom., 5396 hem., cov: 23)
  • Exomes 𝑓: 0.21 (6950 hom. 24976 hem.)
• Consequence: SAT1 NM_002970.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAT1	NM_002970.4	c.-158C>T		5_prime_UTR_variant	1/6	ENST00000379270.5
SAT1	NR_027783.3	n.22C>T		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAT1	ENST00000379270.5	c.-158C>T		5_prime_UTR_variant	1/6	1	NM_002970.4	P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 18744 AN: 111404 Hom.: 1591 Cov.: 23 AF XY: 0.161 AC XY: 5394 AN XY: 33606

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.000843

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.0798

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.208 AC: 79322 AN: 381535 Hom.: 6950 Cov.: 5 AF XY: 0.201 AC XY: 24976 AN XY: 124315

Gnomad4 AFR exome AF: 0.0362

Gnomad4 AMR exome AF: 0.0936

Gnomad4 ASJ exome AF: 0.199

Gnomad4 EAS exome AF: 0.000257

Gnomad4 SAS exome AF: 0.0539

Gnomad4 FIN exome AF: 0.284

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.197

GnomAD4 genome AF: 0.168 AC: 18749 AN: 111455 Hom.: 1592 Cov.: 23 AF XY: 0.160 AC XY: 5396 AN XY: 33667

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.000845

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.154

Alfa AF: 0.227 Hom.: 6213

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	1.9
Dann	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs11550721; hg19: chrX-23801311;