chr6-83019040-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198920.3(UBE3D):c.943G>A(p.Asp315Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,613,664 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_198920.3 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 |
---|---|---|---|---|---|---|---|
UBE3D | NM_198920.3 | c.943G>A | p.Asp315Asn | missense_variant | 8/10 | ENST00000369747.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE3D | ENST00000369747.8 | c.943G>A | p.Asp315Asn | missense_variant | 8/10 | 1 | NM_198920.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 250960Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135656
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461560Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727090
GnomAD4 genome AF: 0.000316 AC: 48AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 20, 2023 | The c.943G>A (p.D315N) alteration is located in exon 8 (coding exon 8) of the UBE3D gene. This alteration results from a G to A substitution at nucleotide position 943, causing the aspartic acid (D) at amino acid position 315 to be replaced by an asparagine (N). 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