rs973213

chr4-107659051-C-T

Variant summary

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

The NM_005443.5(PAPSS1):c.783+908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,262 control chromosomes in the GnomAD database, including 414 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 0.070 (414 hom., cov: 32)
• Consequence: PAPSS1 NM_005443.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAPSS1	NM_005443.5	c.783+908G>A		intron_variant		ENST00000265174.5
PAPSS1	XM_011532400.3	c.720+908G>A		intron_variant
PAPSS1	XM_011532401.2	c.720+908G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAPSS1	ENST00000265174.5	c.783+908G>A		intron_variant		1	NM_005443.5	P1
PAPSS1	ENST00000511304.5	n.475+908G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10666 AN: 152144 Hom.: 413 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0702 AC: 10689 AN: 152262 Hom.: 414 Cov.: 32 AF XY: 0.0673 AC XY: 5007 AN XY: 74446

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0691 Hom.: 148

Bravo AF: 0.0731

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.14
Dann	Benign	0.58

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: rs973213; hg19: chr4-108580207;