18-62113140-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_176787.5(PIGN):āc.1428A>Cā(p.Glu476Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,452,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_176787.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGN | NM_176787.5 | c.1428A>C | p.Glu476Asp | missense_variant | Exon 16 of 31 | ENST00000640252.2 | NP_789744.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGN | ENST00000640252.2 | c.1428A>C | p.Glu476Asp | missense_variant | Exon 16 of 31 | 1 | NM_176787.5 | ENSP00000492233.1 | ||
PIGN | ENST00000400334.7 | c.1428A>C | p.Glu476Asp | missense_variant | Exon 15 of 30 | 1 | ENSP00000383188.2 | |||
PIGN | ENST00000638424.1 | n.1428A>C | non_coding_transcript_exon_variant | Exon 14 of 29 | 5 | ENSP00000491963.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236914Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128160
GnomAD4 exome AF: 0.00000895 AC: 13AN: 1452860Hom.: 0 Cov.: 29 AF XY: 0.0000125 AC XY: 9AN XY: 721942
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at