3-52501268-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015136.3(STAB1):c.181C>T(p.Arg61Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,410 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R61Q) has been classified 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.181C>T | p.Arg61Trp | missense_variant | 2/69 | ENST00000321725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAB1 | ENST00000321725.10 | c.181C>T | p.Arg61Trp | missense_variant | 2/69 | 1 | NM_015136.3 | P1 | |
STAB1 | ENST00000481607.1 | n.236C>T | non_coding_transcript_exon_variant | 2/21 | 1 | ||||
STAB1 | ENST00000479355.1 | n.226C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251072Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135800
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461160Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726874
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2021 | The c.181C>T (p.R61W) alteration is located in exon 2 (coding exon 2) of the STAB1 gene. This alteration results from a C to T substitution at nucleotide position 181, causing the arginine (R) at amino acid position 61 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