16-372016-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021259.3(PGAP6):c.2287G>A(p.Asp763Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,460,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D763Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_021259.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAP6 | ENST00000431232.7 | c.2287G>A | p.Asp763Asn | missense_variant | Exon 13 of 13 | 1 | NM_021259.3 | ENSP00000401338.2 | ||
PGAP6 | ENST00000250930.7 | c.1708G>A | p.Asp570Asn | missense_variant | Exon 13 of 13 | 2 | ENSP00000250930.3 | |||
PGAP6 | ENST00000424078.5 | c.688G>A | p.Asp230Asn | missense_variant | Exon 4 of 4 | 3 | ENSP00000397620.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460384Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726472
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.