4-67701103-G-A
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018227.6(UBA6):c.17C>T(p.Pro6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018227.6 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBA6 | NM_018227.6 | c.17C>T | p.Pro6Leu | missense_variant | Exon 1 of 33 | ENST00000322244.10 | NP_060697.4 | |
UBA6 | XM_017008359.3 | c.17C>T | p.Pro6Leu | missense_variant | Exon 1 of 33 | XP_016863848.1 | ||
UBA6 | XM_047415893.1 | c.17C>T | p.Pro6Leu | missense_variant | Exon 1 of 28 | XP_047271849.1 | ||
UBA6-DT | NR_015439.1 | n.-175G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000802 AC: 2AN: 249248 AF XY: 0.0000148 show subpopulations
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461270Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 726968 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.17C>T (p.P6L) alteration is located in exon 1 (coding exon 1) of the UBA6 gene. This alteration results from a C to T substitution at nucleotide position 17, causing the proline (P) at amino acid position 6 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