rs572992003
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_024989.4(PGAP1):āc.1691T>Cā(p.Leu564Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,613,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024989.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGAP1 | NM_024989.4 | c.1691T>C | p.Leu564Ser | missense_variant | 18/27 | ENST00000354764.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGAP1 | ENST00000354764.9 | c.1691T>C | p.Leu564Ser | missense_variant | 18/27 | 1 | NM_024989.4 | P1 | |
PGAP1 | ENST00000423035.5 | c.*1622T>C | 3_prime_UTR_variant, NMD_transcript_variant | 19/28 | 1 | ||||
PGAP1 | ENST00000409475.5 | c.1691T>C | p.Leu564Ser | missense_variant | 18/20 | 2 | |||
PGAP1 | ENST00000470179.5 | n.1155T>C | non_coding_transcript_exon_variant | 14/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251226Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135792
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1460682Hom.: 0 Cov.: 29 AF XY: 0.0000633 AC XY: 46AN XY: 726700
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 21, 2016 | - - |
Intellectual disability, autosomal recessive 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at