chr16-681836-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_005861.4(STUB1):c.568G>A(p.Asp190Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,458,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005861.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STUB1 | NM_005861.4 | c.568G>A | p.Asp190Asn | missense_variant | 4/7 | ENST00000219548.9 | |
JMJD8 | NM_001005920.4 | c.*958C>T | 3_prime_UTR_variant | 9/9 | ENST00000609261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STUB1 | ENST00000219548.9 | c.568G>A | p.Asp190Asn | missense_variant | 4/7 | 1 | NM_005861.4 | P1 | |
JMJD8 | ENST00000609261.6 | c.*958C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_001005920.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248818Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134968
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458504Hom.: 0 Cov.: 33 AF XY: 0.00000414 AC XY: 3AN XY: 725190
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 20, 2024 | Variant summary: STUB1 c.568G>A (p.Asp190Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 248818 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.568G>A in individuals affected with Autosomal Recessive Spinocerebellar Ataxia 16 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 2645847). Based on the evidence outlined above, the variant was classified as uncertain significance. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | STUB1: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at