chr16-574551-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004204.5(PIGQ):c.477G>A(p.Thr159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000468 in 1,603,890 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. T159T) has been classified as Likely benign.
Frequency
Consequence
NM_004204.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGQ | NM_004204.5 | c.477G>A | p.Thr159= | synonymous_variant | 2/11 | ENST00000321878.10 | |
PIGQ | NM_148920.4 | c.477G>A | p.Thr159= | synonymous_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.477G>A | p.Thr159= | synonymous_variant | 2/11 | 1 | NM_004204.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152208Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000622 AC: 14AN: 225136Hom.: 0 AF XY: 0.0000567 AC XY: 7AN XY: 123408
GnomAD4 exome AF: 0.0000420 AC: 61AN: 1451564Hom.: 0 Cov.: 40 AF XY: 0.0000360 AC XY: 26AN XY: 721288
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152326Hom.: 0 Cov.: 34 AF XY: 0.000121 AC XY: 9AN XY: 74490
ClinVar
Submissions by phenotype
Epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at