3-49808027-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003335.3(UBA7):c.2516G>A(p.Arg839His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000366 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R839P) has been classified as Benign.
Frequency
Consequence
NM_003335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000291 AC: 73AN: 250752Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135614
GnomAD4 exome AF: 0.000369 AC: 540AN: 1461748Hom.: 1 Cov.: 31 AF XY: 0.000355 AC XY: 258AN XY: 727174
GnomAD4 genome AF: 0.000335 AC: 51AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2516G>A (p.R839H) alteration is located in exon 20 (coding exon 20) of the UBA7 gene. This alteration results from a G to A substitution at nucleotide position 2516, causing the arginine (R) at amino acid position 839 to be replaced by a histidine (H). 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