19-4446388-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_025241.3(UBXN6):c.946G>C(p.Val316Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,577,024 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBXN6 | NM_025241.3 | c.946G>C | p.Val316Leu | missense_variant | 9/11 | ENST00000301281.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBXN6 | ENST00000301281.11 | c.946G>C | p.Val316Leu | missense_variant | 9/11 | 1 | NM_025241.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000892 AC: 17AN: 190602Hom.: 0 AF XY: 0.0000572 AC XY: 6AN XY: 104890
GnomAD4 exome AF: 0.000188 AC: 268AN: 1424676Hom.: 4 Cov.: 32 AF XY: 0.000171 AC XY: 121AN XY: 707600
GnomAD4 genome ? AF: 0.000203 AC: 31AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.946G>C (p.V316L) alteration is located in exon 9 (coding exon 9) of the UBXN6 gene. This alteration results from a G to C substitution at nucleotide position 946, causing the valine (V) at amino acid position 316 to be replaced by a leucine (L). 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