chr8-144082792-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003801.4(GPAA1):āc.62A>Gā(p.Asn21Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000614 in 1,464,998 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 Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. N21N) has been classified as Likely benign.
Frequency
Consequence
NM_003801.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPAA1 | NM_003801.4 | c.62A>G | p.Asn21Ser | missense_variant | 1/12 | ENST00000355091.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPAA1 | ENST00000355091.9 | c.62A>G | p.Asn21Ser | missense_variant | 1/12 | 1 | NM_003801.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151994Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000533 AC: 7AN: 1313004Hom.: 0 Cov.: 31 AF XY: 0.00000774 AC XY: 5AN XY: 646280
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151994Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74248
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GPAA1 protein function. ClinVar contains an entry for this variant (Variation ID: 1958455). This variant has not been reported in the literature in individuals affected with GPAA1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.1%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 21 of the GPAA1 protein (p.Asn21Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at