12-64713671-T-TAA
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002076.4(GNS):c.*3068_*3069dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 152,214 control chromosomes in the GnomAD database, including 494 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.043 ( 494 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GNS
NM_002076.4 3_prime_UTR
NM_002076.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.489
Genes affected
GNS (HGNC:4422): (glucosamine (N-acetyl)-6-sulfatase) The product of this gene is a lysosomal enzyme found in all cells. It is involved in the catabolism of heparin, heparan sulphate, and keratan sulphate. Deficiency of this enzyme results in the accumulation of undegraded substrate and the lysosomal storage disorder mucopolysaccharidosis type IIID (Sanfilippo D syndrome). Mucopolysaccharidosis type IIID is the least common of the four subtypes of Sanfilippo syndrome. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-64713671-T-TAA is Benign according to our data. Variant chr12-64713671-T-TAA is described in ClinVar as [Likely_benign]. Clinvar id is 310163.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNS | NM_002076.4 | c.*3068_*3069dupTT | 3_prime_UTR_variant | 14/14 | ENST00000258145.8 | NP_002067.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0431 AC: 6549AN: 152096Hom.: 492 Cov.: 32
GnomAD3 genomes
AF:
AC:
6549
AN:
152096
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 298Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 188
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
298
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
188
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0431 AC: 6566AN: 152214Hom.: 494 Cov.: 32 AF XY: 0.0412 AC XY: 3063AN XY: 74430
GnomAD4 genome
AF:
AC:
6566
AN:
152214
Hom.:
Cov.:
32
AF XY:
AC XY:
3063
AN XY:
74430
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:
Asia WGS
AF:
AC:
22
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Sanfilippo syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at