chr20-45419334-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 3P and 16B. PM1PP3BP6_Very_StrongBA1
The NM_015937.6(PIGT):c.533G>A(p.Arg178Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00404 in 1,614,094 control chromosomes in the GnomAD database, including 330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R178W) has been classified as Uncertain significance.
Frequency
Consequence
NM_015937.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGT | NM_015937.6 | c.533G>A | p.Arg178Gln | missense_variant | 4/12 | ENST00000279036.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGT | ENST00000279036.12 | c.533G>A | p.Arg178Gln | missense_variant | 4/12 | 1 | NM_015937.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00455 AC: 693AN: 152212Hom.: 21 Cov.: 33
GnomAD3 exomes AF: 0.0170 AC: 4276AN: 251278Hom.: 250 AF XY: 0.0126 AC XY: 1716AN XY: 135794
GnomAD4 exome AF: 0.00398 AC: 5819AN: 1461764Hom.: 308 Cov.: 31 AF XY: 0.00345 AC XY: 2507AN XY: 727190
GnomAD4 genome AF: 0.00457 AC: 696AN: 152330Hom.: 22 Cov.: 33 AF XY: 0.00466 AC XY: 347AN XY: 74488
ClinVar
Submissions by phenotype
Multiple congenital anomalies-hypotonia-seizures syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 25, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at