rs3217087

Variant names:

• chr10-87659881-CGCTGCTGCTGCT-C
• NM_001015880.2:c.-86_-75delTGCTGCTGCTGC

Your query was ambiguous. Multiple possible variants found:

• chr10-87659881-CGCTGCTGCTGCT-C
• chr10-87659881-CGCTGCTGCTGCT-CGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCTGCCGCCGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
• chr10-87659881-CGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001015880.2(PAPSS2):​c.-86_-75delTGCTGCTGCTGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 886,570 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000024 (0 hom.)
• Consequence: PAPSS2 NM_001015880.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

Genes affected

PAPSS2 (HGNC:8604): (3'-phosphoadenosine 5'-phosphosulfate synthase 2) Sulfation is a common modification of endogenous (lipids, proteins, and carbohydrates) and exogenous (xenobiotics and drugs) compounds. In mammals, the sulfate source is 3'-phosphoadenosine 5'-phosphosulfate (PAPS), created from ATP and inorganic sulfate. Two different tissue isoforms encoded by different genes synthesize PAPS. This gene encodes one of the two PAPS synthetases. Defects in this gene cause the Pakistani type of spondyloepimetaphyseal dysplasia. Two alternatively spliced transcript variants that encode different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ENSG00000196566 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAPSS2	NM_001015880.2	c.-86_-75delTGCTGCTGCTGC		5_prime_UTR_variant	Exon 1 of 13	ENST00000456849.2	NP_001015880.1
PAPSS2	NM_004670.4	c.-86_-75delTGCTGCTGCTGC		5_prime_UTR_variant	Exon 1 of 12		NP_004661.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAPSS2	ENST00000456849	c.-86_-75delTGCTGCTGCTGC		5_prime_UTR_variant	Exon 1 of 13	1	NM_001015880.2	ENSP00000406157.1
PAPSS2	ENST00000361175	c.-86_-75delTGCTGCTGCTGC		5_prime_UTR_variant	Exon 1 of 12	1		ENSP00000354436.4
ENSG00000196566	ENST00000354527.2	n.111_122delAGCAGCAGCAGC		non_coding_transcript_exon_variant	Exon 1 of 4	3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000237 AC: 21 AN: 886570 Hom.: 0 AF XY: 0.0000239 AC XY: 11 AN XY: 460176

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000348

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-89419638;