chr2-48580809-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006873.4(STON1):c.176G>A(p.Ser59Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,551,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006873.4 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 |
---|---|---|---|---|---|---|---|
STON1 | NM_006873.4 | c.176G>A | p.Ser59Asn | missense_variant | 2/4 | ENST00000404752.6 | |
STON1-GTF2A1L | NM_001198593.2 | c.176G>A | p.Ser59Asn | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STON1 | ENST00000404752.6 | c.176G>A | p.Ser59Asn | missense_variant | 2/4 | 1 | NM_006873.4 | P1 | |
STON1 | ENST00000406226.1 | c.176G>A | p.Ser59Asn | missense_variant | 3/5 | 1 | P1 | ||
STON1 | ENST00000649748.1 | c.176G>A | p.Ser59Asn | missense_variant | 3/5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000111 AC: 22AN: 197390Hom.: 0 AF XY: 0.0000950 AC XY: 10AN XY: 105290
GnomAD4 exome AF: 0.0000372 AC: 52AN: 1399498Hom.: 0 Cov.: 36 AF XY: 0.0000362 AC XY: 25AN XY: 690920
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.176G>A (p.S59N) alteration is located in exon 3 (coding exon 1) of the STON1 gene. This alteration results from a G to A substitution at nucleotide position 176, causing the serine (S) at amino acid position 59 to be replaced by an asparagine (N). 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