rs2076484
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006398.4(UBD):āc.152T>Cā(p.Leu51Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 1,612,944 control chromosomes in the GnomAD database, including 10,453 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006398.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBD | NM_006398.4 | c.152T>C | p.Leu51Ser | missense_variant | 2/2 | ENST00000377050.5 | |
OR2I1P | NM_001396058.1 | c.*2060A>G | 3_prime_UTR_variant | 2/2 | ENST00000641137.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBD | ENST00000377050.5 | c.152T>C | p.Leu51Ser | missense_variant | 2/2 | 1 | NM_006398.4 | P1 | |
OR2I1P | ENST00000641137.2 | c.*2060A>G | 3_prime_UTR_variant | 2/2 | NM_001396058.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23922AN: 152078Hom.: 4367 Cov.: 32
GnomAD3 exomes AF: 0.0819 AC: 20203AN: 246596Hom.: 2271 AF XY: 0.0774 AC XY: 10407AN XY: 134380
GnomAD4 exome AF: 0.0464 AC: 67846AN: 1460748Hom.: 6054 Cov.: 35 AF XY: 0.0479 AC XY: 34842AN XY: 726688
GnomAD4 genome ? AF: 0.158 AC: 23998AN: 152196Hom.: 4399 Cov.: 32 AF XY: 0.156 AC XY: 11614AN XY: 74426
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at