NM_004287.5:c.322A>C
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_004287.5(GOSR2):āc.322A>Cā(p.Thr108Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000169 in 1,614,052 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004287.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOSR2 | ENST00000640051.2 | c.322A>C | p.Thr108Pro | missense_variant | Exon 4 of 6 | 1 | NM_004287.5 | ENSP00000492751.1 | ||
ENSG00000262633 | ENST00000571841.1 | n.322A>C | non_coding_transcript_exon_variant | Exon 4 of 10 | 5 | ENSP00000461460.1 |
Frequencies
GnomAD3 genomes AF: 0.000993 AC: 151AN: 152130Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000243 AC: 61AN: 250880 AF XY: 0.000214 show subpopulations
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727200 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000992 AC: 151AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000981 AC XY: 73AN XY: 74436 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Uncertain:3
BP4 -
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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Inborn genetic diseases Uncertain:1
The p.T108P variant (also known as c.322A>C), located in coding exon 4 of the GOSR2 gene, results from an A to C substitution at nucleotide position 322. The threonine at codon 108 is replaced by proline, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Progressive myoclonic epilepsy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at