rs112454391
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BS1BS2
The NM_000512.5(GALNS):c.359C>T(p.Ser120Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000735 in 1,613,256 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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. S120S) has been classified as Likely benign.
Frequency
Consequence
NM_000512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNS | NM_000512.5 | c.359C>T | p.Ser120Leu | missense_variant | 4/14 | ENST00000268695.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNS | ENST00000268695.10 | c.359C>T | p.Ser120Leu | missense_variant | 4/14 | 1 | NM_000512.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00372 AC: 566AN: 152146Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00108 AC: 270AN: 251006Hom.: 3 AF XY: 0.000743 AC XY: 101AN XY: 135856
GnomAD4 exome AF: 0.000424 AC: 620AN: 1460992Hom.: 6 Cov.: 31 AF XY: 0.000367 AC XY: 267AN XY: 726810
GnomAD4 genome ? AF: 0.00372 AC: 566AN: 152264Hom.: 3 Cov.: 33 AF XY: 0.00345 AC XY: 257AN XY: 74450
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-IV-A Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | research | Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova | Feb 01, 2021 | Allele frequency is greater than expected for disorder (BS1_strong) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at