chr10-87659914-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001015880.2(PAPSS2):c.-68C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00299 in 1,548,534 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.016 ( 72 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 62 hom. )
Consequence
PAPSS2
NM_001015880.2 5_prime_UTR
NM_001015880.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.144
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 10-87659914-C-T is Benign according to our data. Variant chr10-87659914-C-T is described in ClinVar as [Benign]. Clinvar id is 1279508.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0586 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAPSS2 | NM_001015880.2 | c.-68C>T | 5_prime_UTR_variant | 1/13 | ENST00000456849.2 | ||
PAPSS2 | NM_004670.4 | c.-68C>T | 5_prime_UTR_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAPSS2 | ENST00000456849.2 | c.-68C>T | 5_prime_UTR_variant | 1/13 | 1 | NM_001015880.2 | A1 | ||
PAPSS2 | ENST00000361175.8 | c.-68C>T | 5_prime_UTR_variant | 1/12 | 1 | P4 | |||
ENST00000354527.2 | n.90G>A | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0164 AC: 2440AN: 148384Hom.: 72 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2440
AN:
148384
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00156 AC: 2191AN: 1400038Hom.: 62 Cov.: 27 AF XY: 0.00135 AC XY: 942AN XY: 698474
GnomAD4 exome
AF:
AC:
2191
AN:
1400038
Hom.:
Cov.:
27
AF XY:
AC XY:
942
AN XY:
698474
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0165 AC: 2444AN: 148496Hom.: 72 Cov.: 32 AF XY: 0.0157 AC XY: 1137AN XY: 72590
GnomAD4 genome
?
AF:
AC:
2444
AN:
148496
Hom.:
Cov.:
32
AF XY:
AC XY:
1137
AN XY:
72590
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 14, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at