chr17-36537155-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001346754.2(PIGW):c.54C>T(p.Thr18Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,088 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. T18T) has been classified as Likely benign.
Frequency
Consequence
NM_001346754.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGW | NM_001346754.2 | c.54C>T | p.Thr18Thr | synonymous_variant | Exon 2 of 2 | ENST00000614443.2 | NP_001333683.1 | |
PIGW | NM_001346755.2 | c.54C>T | p.Thr18Thr | synonymous_variant | Exon 2 of 2 | NP_001333684.1 | ||
PIGW | NM_178517.5 | c.54C>T | p.Thr18Thr | synonymous_variant | Exon 2 of 2 | NP_848612.2 | ||
MYO19 | XM_047436823.1 | c.-295-3051G>A | intron_variant | Intron 2 of 29 | XP_047292779.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250072Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135146
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460760Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726642
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74480
ClinVar
Submissions by phenotype
Hyperphosphatasia with intellectual disability syndrome 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at