chr9-78297214-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_058179.4(PSAT1):c.4G>A(p.Asp2Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000687 in 1,600,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D2Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_058179.4 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 |
---|---|---|---|---|---|---|---|
PSAT1 | NM_058179.4 | c.4G>A | p.Asp2Asn | missense_variant | 1/9 | ENST00000376588.4 | |
PSAT1 | NM_021154.5 | c.4G>A | p.Asp2Asn | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSAT1 | ENST00000376588.4 | c.4G>A | p.Asp2Asn | missense_variant | 1/9 | 1 | NM_058179.4 | P1 | |
PSAT1 | ENST00000347159.6 | c.4G>A | p.Asp2Asn | missense_variant | 1/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000879 AC: 2AN: 227580Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124734
GnomAD4 exome AF: 0.00000621 AC: 9AN: 1448666Hom.: 0 Cov.: 36 AF XY: 0.00000833 AC XY: 6AN XY: 720518
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
Neu-Laxova syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 10, 2022 | This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 2 of the PSAT1 protein (p.Asp2Asn). 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. Experimental studies have shown that this missense change does not substantially affect PSAT1 function (PMID: 32077105). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 976916). This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. - |
not provided Other:1
not provided, no classification provided | in vivo;research | Dudley Research Group, Pacific Northwest Research Institute | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at