rs1147096
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_002076.4(GNS):c.198G>T(p.Pro66=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000756 in 1,455,412 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P66P) has been classified as Benign.
Frequency
Consequence
NM_002076.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNS | NM_002076.4 | c.198G>T | p.Pro66= | synonymous_variant | 2/14 | ENST00000258145.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNS | ENST00000258145.8 | c.198G>T | p.Pro66= | synonymous_variant | 2/14 | 1 | NM_002076.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 245972Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132960
GnomAD4 exome AF: 0.00000614 AC: 8AN: 1303236Hom.: 0 Cov.: 22 AF XY: 0.0000107 AC XY: 7AN XY: 656348
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-D Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at