17-36537108-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001346754.2(PIGW):c.7G>A(p.Glu3Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,584,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001346754.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGW | NM_001346754.2 | c.7G>A | p.Glu3Lys | missense_variant | 2/2 | ENST00000614443.2 | |
PIGW | NM_001346755.2 | c.7G>A | p.Glu3Lys | missense_variant | 2/2 | ||
PIGW | NM_178517.5 | c.7G>A | p.Glu3Lys | missense_variant | 2/2 | ||
MYO19 | XM_047436823.1 | c.-295-3004C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGW | ENST00000614443.2 | c.7G>A | p.Glu3Lys | missense_variant | 2/2 | 1 | NM_001346754.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 228732Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123796
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1432628Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 710866
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.7G>A (p.E3K) alteration is located in exon 2 (coding exon 1) of the PIGW gene. This alteration results from a G to A substitution at nucleotide position 7, causing the glutamic acid (E) at amino acid position 3 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at