rs9332468

Variant names:

• chr4-107597943-A-G
• rs9332468
• ENST00000514815.1:n.175-7546T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-107597943-A-G
• chr4-107597943-A-T

Variant summary

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

The ENST00000514815.1(PAPSS1):​n.175-7546T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,142 control chromosomes in the GnomAD database, including 5,998 homozygotes. 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 0.28 (5998 hom., cov: 32)
• Consequence: PAPSS1 ENST00000514815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367

Genes affected

PAPSS1 (HGNC:8603): (3'-phosphoadenosine 5'-phosphosulfate synthase 1) Three-prime-phosphoadenosine 5-prime-phosphosulfate (PAPS) is the sulfate donor cosubstrate for all sulfotransferase (SULT) enzymes (Xu et al., 2000 [PubMed 10679223]). SULTs catalyze the sulfate conjugation of many endogenous and exogenous compounds, including drugs and other xenobiotics. In humans, PAPS is synthesized from adenosine 5-prime triphosphate (ATP) and inorganic sulfate by 2 isoforms, PAPSS1 and PAPSS2 (MIM 603005).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAPSS1	ENST00000514815.1	n.175-7546T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42642 AN: 152024 Hom.: 5980 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.281 AC: 42700 AN: 152142 Hom.: 5998 Cov.: 32 AF XY: 0.280 AC XY: 20826 AN XY: 74384

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.282

Alfa AF: 0.271 Hom.: 1177

Bravo AF: 0.291

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332468; hg19: chr4-108519099;