5-172211996-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152277.3(UBTD2):c.539G>A(p.Arg180Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBTD2 | NM_152277.3 | c.539G>A | p.Arg180Gln | missense_variant | Exon 3 of 3 | ENST00000393792.3 | NP_689490.2 | |
UBTD2 | XM_017010022.2 | c.407G>A | p.Arg136Gln | missense_variant | Exon 3 of 3 | XP_016865511.1 | ||
UBTD2 | XM_047417875.1 | c.407G>A | p.Arg136Gln | missense_variant | Exon 3 of 3 | XP_047273831.1 | ||
UBTD2 | XM_047417876.1 | c.407G>A | p.Arg136Gln | missense_variant | Exon 4 of 4 | XP_047273832.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251388Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135864
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727242
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.539G>A (p.R180Q) alteration is located in exon 3 (coding exon 3) of the UBTD2 gene. This alteration results from a G to A substitution at nucleotide position 539, causing the arginine (R) at amino acid position 180 to be replaced by a glutamine (Q). 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