3-52501744-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015136.3(STAB1):c.322C>T(p.Arg108Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 1,561,956 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_015136.3 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 |
---|---|---|---|---|---|---|---|
STAB1 | NM_015136.3 | c.322C>T | p.Arg108Trp | missense_variant | 3/69 | ENST00000321725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAB1 | ENST00000321725.10 | c.322C>T | p.Arg108Trp | missense_variant | 3/69 | 1 | NM_015136.3 | P1 | |
STAB1 | ENST00000481607.1 | n.377C>T | non_coding_transcript_exon_variant | 3/21 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000155 AC: 26AN: 167576Hom.: 0 AF XY: 0.000134 AC XY: 12AN XY: 89312
GnomAD4 exome AF: 0.000338 AC: 476AN: 1409790Hom.: 0 Cov.: 32 AF XY: 0.000332 AC XY: 231AN XY: 696698
GnomAD4 genome AF: 0.000230 AC: 35AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.322C>T (p.R108W) alteration is located in exon 3 (coding exon 3) of the STAB1 gene. This alteration results from a C to T substitution at nucleotide position 322, causing the arginine (R) at amino acid position 108 to be replaced by a tryptophan (W). 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