chr8-43140516-CGCTGGCCGCGCTGCT-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_152419.3(HGSNAT):c.31_45del(p.Leu11_Ala15del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 1,079,848 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.
Frequency
Consequence
NM_152419.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.31_45del | p.Leu11_Ala15del | inframe_deletion | 1/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.31_45del | p.Leu11_Ala15del | inframe_deletion | 1/18 | 2 | NM_152419.3 | P3 | |
HGSNAT | ENST00000520704.1 | c.-120_-106del | 5_prime_UTR_variant, NMD_transcript_variant | 1/10 | 1 | ||||
HGSNAT | ENST00000517319.1 | c.31_45del | p.Leu11_Ala15del | inframe_deletion, NMD_transcript_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000135 AC: 2AN: 147980Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000107 AC: 10AN: 931868Hom.: 0 AF XY: 0.0000114 AC XY: 5AN XY: 438126
GnomAD4 genome ? AF: 0.0000135 AC: 2AN: 147980Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72084
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Aug 23, 2017 | - - |
Mucopolysaccharidosis, MPS-III-C;C4225287:Retinitis pigmentosa 73 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | This variant, c.31_45del, results in the deletion of 5 amino acid(s) of the HGSNAT protein (p.Leu11_Ala15del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with HGSNAT-related conditions. ClinVar contains an entry for this variant (Variation ID: 553290). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at