chr8-43140506-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_152419.3(HGSNAT):c.10G>C(p.Ala4Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000715 in 1,048,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A4A) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.10G>C | p.Ala4Pro | missense_variant | 1/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.10G>C | p.Ala4Pro | missense_variant | 1/18 | 2 | NM_152419.3 | P3 | |
HGSNAT | ENST00000520704.1 | c.-141G>C | 5_prime_UTR_variant, NMD_transcript_variant | 1/10 | 1 | ||||
HGSNAT | ENST00000517319.1 | c.10G>C | p.Ala4Pro | missense_variant, NMD_transcript_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000406 AC: 6AN: 147748Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000766 AC: 69AN: 901050Hom.: 0 Cov.: 29 AF XY: 0.0000711 AC XY: 30AN XY: 421998
GnomAD4 genome ? AF: 0.0000406 AC: 6AN: 147748Hom.: 0 Cov.: 32 AF XY: 0.0000556 AC XY: 4AN XY: 71966
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-C;C4225287:Retinitis pigmentosa 73 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at