4-107609729-C-T

Variant names:

• chr4-107609729-C-T
• rs1514730
• ENST00000514815.1:n.175-19332G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514815.1(PAPSS1):​n.175-19332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,932 control chromosomes in the GnomAD database, including 10,059 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 0.36 (10059 hom., cov: 32)
• Consequence: PAPSS1 ENST00000514815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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.175-19332G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54545 AN: 151814 Hom.: 10037 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.359 AC: 54614 AN: 151932 Hom.: 10059 Cov.: 32 AF XY: 0.354 AC XY: 26317 AN XY: 74238

African (AFR) AF: 0.452 AC: 18721 AN: 41416

American (AMR) AF: 0.348 AC: 5311 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2491 AN: 5152

South Asian (SAS) AF: 0.199 AC: 957 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21710 AN: 67972

Other (OTH) AF: 0.390 AC: 823 AN: 2108

Alfa AF: 0.332 Hom.: 35963

Bravo AF: 0.375

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.1
DANN	Benign	0.79
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1514730; hg19: chr4-108530885;