chr1-229636946-T-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014777.4(URB2):āc.2333T>Gā(p.Val778Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,613,694 control chromosomes in the GnomAD database, including 227,612 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_014777.4 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 |
---|---|---|---|---|---|---|---|
URB2 | NM_014777.4 | c.2333T>G | p.Val778Gly | missense_variant | 4/10 | ENST00000258243.7 | |
URB2 | NM_001314021.2 | c.2333T>G | p.Val778Gly | missense_variant | 4/10 | ||
URB2 | XM_005273360.3 | c.2333T>G | p.Val778Gly | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
URB2 | ENST00000258243.7 | c.2333T>G | p.Val778Gly | missense_variant | 4/10 | 1 | NM_014777.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.534 AC: 81222AN: 152022Hom.: 21931 Cov.: 34
GnomAD3 exomes AF: 0.560 AC: 140545AN: 251004Hom.: 40296 AF XY: 0.555 AC XY: 75238AN XY: 135682
GnomAD4 exome AF: 0.527 AC: 770296AN: 1461554Hom.: 205656 Cov.: 73 AF XY: 0.528 AC XY: 383855AN XY: 727066
GnomAD4 genome AF: 0.534 AC: 81302AN: 152140Hom.: 21956 Cov.: 34 AF XY: 0.544 AC XY: 40460AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at