3-3982184-A-G

Variant names:

• chr3-3982184-A-G
• rs1385467
• ENST00000450418.1:n.2112T>C

Variant summary

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

The ENST00000450418.1(PNPT1P1):​n.2112T>C 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 0.341 in 711,242 control chromosomes in the GnomAD database, including 52,801 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 0.39 (14411 hom., cov: 33)
  • Exomes 𝑓: 0.33 (38390 hom.)
• Consequence: PNPT1P1 ENST00000450418.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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.2112T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
SUMF1	ENST00000448413.5	n.1191+86385T>C		intron_variant	Intron 9 of 12	2		ENSP00000404384.1
ENSG00000287720	ENST00000661097.1	n.131-20245A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58970 AN: 151974 Hom.: 14368 Cov.: 33

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.328 AC: 183395 AN: 559150 Hom.: 38390 Cov.: 6 AF XY: 0.333 AC XY: 102064 AN XY: 306776

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.276

Gnomad4 EAS exome AF: 0.799

Gnomad4 SAS exome AF: 0.511

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.232

Gnomad4 OTH exome AF: 0.321

GnomAD4 genome AF: 0.388 AC: 59076 AN: 152092 Hom.: 14411 Cov.: 33 AF XY: 0.391 AC XY: 29076 AN XY: 74336

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.375

Alfa AF: 0.301 Hom.: 1944

Bravo AF: 0.414

Asia WGS AF: 0.651 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.67
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1385467; hg19: chr3-4023868;