rs1353819

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

SUMF1 Gene-Disease associations (from GenCC):

• mucosulfatidosis

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen, G2P

ENSG00000287720 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450418.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNPT1P1	ENST00000450418.1	TSL:6	n.1914A>G		non_coding_transcript_exon	Exon 1 of 1
	SUMF1	ENST00000448413.5	TSL:2	n.1191+86187A>G		intron	N/A	ENSP00000404384.1
	ENSG00000287720	ENST00000661097.1		n.131-20047T>C		intron	N/A

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

African (AFR) AF: 0.252 AC: 7623 AN: 30268

American (AMR) AF: 0.383 AC: 16893 AN: 44052

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 5048 AN: 24664

East Asian (EAS) AF: 0.441 AC: 17149 AN: 38854

South Asian (SAS) AF: 0.252 AC: 20962 AN: 83340

European-Finnish (FIN) AF: 0.0820 AC: 4248 AN: 51820

Middle Eastern (MID) AF: 0.184 AC: 718 AN: 3910

European-Non Finnish (NFE) AF: 0.167 AC: 162147 AN: 971486

Other (OTH) AF: 0.195 AC: 10600 AN: 54454

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

African (AFR) AF: 0.235 AC: 9767 AN: 41490

American (AMR) AF: 0.298 AC: 4559 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2079 AN: 5156

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4820

European-Finnish (FIN) AF: 0.0722 AC: 767 AN: 10618

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10301 AN: 68006

Other (OTH) AF: 0.204 AC: 432 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.27
DANN	Benign	0.58
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1353819; hg19: chr3-4024066;