rs73675469
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152419.3(HGSNAT):c.1840G>A(p.Val614Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,611,490 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V614V) has been classified as Likely benign.
Frequency
Consequence
NM_152419.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.1840G>A | p.Val614Ile | missense_variant | 18/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.1840G>A | p.Val614Ile | missense_variant | 18/18 | 2 | NM_152419.3 | P3 | |
HGSNAT | ENST00000519705.1 | n.1156G>A | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
HGSNAT | ENST00000521576.1 | c.991G>A | p.Val331Ile | missense_variant | 9/9 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0232 AC: 3535AN: 152086Hom.: 132 Cov.: 32
GnomAD3 exomes AF: 0.00704 AC: 1741AN: 247236Hom.: 61 AF XY: 0.00619 AC XY: 828AN XY: 133846
GnomAD4 exome AF: 0.00305 AC: 4445AN: 1459286Hom.: 159 Cov.: 32 AF XY: 0.00293 AC XY: 2129AN XY: 725686
GnomAD4 genome ? AF: 0.0233 AC: 3548AN: 152204Hom.: 132 Cov.: 32 AF XY: 0.0233 AC XY: 1737AN XY: 74422
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-C Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Benign:2
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Sep 21, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 23, 2013 | - - |
Mucopolysaccharidosis, MPS-III-C;C4225287:Retinitis pigmentosa 73 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at