chr19-4446539-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025241.3(UBXN6):c.881A>G(p.Asn294Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,612,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025241.3 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 |
---|---|---|---|---|---|---|---|
UBXN6 | NM_025241.3 | c.881A>G | p.Asn294Ser | missense_variant | 8/11 | ENST00000301281.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBXN6 | ENST00000301281.11 | c.881A>G | p.Asn294Ser | missense_variant | 8/11 | 1 | NM_025241.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000692 AC: 17AN: 245764Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 133902
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1459814Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726296
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.881A>G (p.N294S) alteration is located in exon 8 (coding exon 8) of the UBXN6 gene. This alteration results from a A to G substitution at nucleotide position 881, causing the asparagine (N) at amino acid position 294 to be replaced by a serine (S). 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