8-43140502-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_152419.3(HGSNAT):c.6C>A(p.Ser2Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,040,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S2S) has been classified as Likely benign.
Frequency
Consequence
NM_152419.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.6C>A | p.Ser2Arg | missense_variant | 1/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.6C>A | p.Ser2Arg | missense_variant | 1/18 | 2 | NM_152419.3 | P3 | |
HGSNAT | ENST00000517319.1 | c.6C>A | p.Ser2Arg | missense_variant, NMD_transcript_variant | 1/5 | 4 | |||
HGSNAT | ENST00000520704.1 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000743 AC: 11AN: 148028Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000112 AC: 1AN: 892530Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 417534
GnomAD4 genome ? AF: 0.0000743 AC: 11AN: 148136Hom.: 0 Cov.: 32 AF XY: 0.000111 AC XY: 8AN XY: 72204
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.6C>A (p.S2R) alteration is located in exon 1 (coding exon 1) of the HGSNAT gene. This alteration results from a C to A substitution at nucleotide position 6, causing the serine (S) at amino acid position 2 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Mucopolysaccharidosis, MPS-III-C;C4225287:Retinitis pigmentosa 73 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at