6-42605721-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001363705.2(UBR2):c.663A>G(p.Val221Val) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,444,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001363705.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBR2 | NM_001363705.2 | c.663A>G | p.Val221Val | splice_region_variant, synonymous_variant | Exon 6 of 47 | ENST00000372901.2 | NP_001350634.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBR2 | ENST00000372901.2 | c.663A>G | p.Val221Val | splice_region_variant, synonymous_variant | Exon 6 of 47 | 5 | NM_001363705.2 | ENSP00000361992.1 | ||
UBR2 | ENST00000372899.6 | c.663A>G | p.Val221Val | splice_region_variant, synonymous_variant | Exon 6 of 47 | 1 | ENSP00000361990.1 | |||
UBR2 | ENST00000372903.6 | c.663A>G | p.Val221Val | splice_region_variant, synonymous_variant | Exon 6 of 12 | 1 | ENSP00000361994.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1444046Hom.: 0 Cov.: 30 AF XY: 0.00000279 AC XY: 2AN XY: 717948
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
UBR2: PM2:Supporting, BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at