chr4-174643970-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006529.4(GLRA3):c.1211A>G(p.Asn404Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,613,788 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006529.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA3 | NM_006529.4 | c.1211A>G | p.Asn404Ser | missense_variant | 10/10 | ENST00000274093.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA3 | ENST00000274093.8 | c.1211A>G | p.Asn404Ser | missense_variant | 10/10 | 1 | NM_006529.4 | ||
GLRA3 | ENST00000340217.5 | c.1166A>G | p.Asn389Ser | missense_variant | 9/9 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251092Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135678
GnomAD4 exome AF: 0.000220 AC: 322AN: 1461692Hom.: 1 Cov.: 31 AF XY: 0.000206 AC XY: 150AN XY: 727176
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.1211A>G (p.N404S) alteration is located in exon 10 (coding exon 10) of the GLRA3 gene. This alteration results from a A to G substitution at nucleotide position 1211, causing the asparagine (N) at amino acid position 404 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at