16-680569-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000219548.9(STUB1):c.44C>T(p.Ala15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000667 in 1,379,380 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. A15S) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000219548.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STUB1 | NM_005861.4 | c.44C>T | p.Ala15Val | missense_variant | 1/7 | ENST00000219548.9 | NP_005852.2 | |
STUB1 | NM_001293197.2 | c.-262C>T | 5_prime_UTR_variant | 1/7 | NP_001280126.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STUB1 | ENST00000219548.9 | c.44C>T | p.Ala15Val | missense_variant | 1/7 | 1 | NM_005861.4 | ENSP00000219548 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000926 AC: 14AN: 151202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000776 AC: 7AN: 90184Hom.: 0 AF XY: 0.0000575 AC XY: 3AN XY: 52168
GnomAD4 exome AF: 0.0000635 AC: 78AN: 1228178Hom.: 0 Cov.: 31 AF XY: 0.0000497 AC XY: 30AN XY: 603786
GnomAD4 genome AF: 0.0000926 AC: 14AN: 151202Hom.: 0 Cov.: 32 AF XY: 0.0000948 AC XY: 7AN XY: 73878
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | STUB1: PM2:Supporting - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 22, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 1879317). This variant has not been reported in the literature in individuals affected with STUB1-related conditions. This variant is present in population databases (rs770617507, gnomAD 0.02%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 15 of the STUB1 protein (p.Ala15Val). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at