rs1353819

Variant names:

• chr3-3982382-T-C
• rs1353819
• ENST00000450418.1:n.1914A>G

Variant summary

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

The ENST00000450418.1(PNPT1P1):​n.1914A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,455,008 control chromosomes in the GnomAD database, including 32,104 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 0.20 (3387 hom., cov: 33)
  • Exomes 𝑓: 0.19 (28717 hom.)
• Consequence: PNPT1P1 ENST00000450418.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

PNPT1P1 (HGNC:44468): (polyribonucleotide nucleotidyltransferase 1 pseudogene 1)

SUMF1 (HGNC:20376): (sulfatase modifying factor 1) This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

ENSG00000287720 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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
PNPT1P1	ENST00000450418.1	n.1914A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
SUMF1	ENST00000448413.5	n.1191+86187A>G		intron_variant	Intron 9 of 12	2		ENSP00000404384.1
ENSG00000287720	ENST00000661097.1	n.131-20047T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29870 AN: 152042 Hom.: 3383 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.188 AC: 245388 AN: 1302848 Hom.: 28717 Cov.: 25 AF XY: 0.188 AC XY: 123178 AN XY: 654538

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.0820

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.197 AC: 29902 AN: 152160 Hom.: 3387 Cov.: 33 AF XY: 0.196 AC XY: 14605 AN XY: 74384

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.204

Alfa AF: 0.174 Hom.: 303

Bravo AF: 0.217

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.27
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353819; hg19: chr3-4024066;