chr21-42088327-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001004416.3(UMODL1):c.637G>A(p.Val213Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,613,646 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 Likely benign (★).
Frequency
Consequence
NM_001004416.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMODL1 | NM_001004416.3 | c.637G>A | p.Val213Ile | missense_variant | 5/23 | ENST00000408910.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMODL1 | ENST00000408910.7 | c.637G>A | p.Val213Ile | missense_variant | 5/23 | 1 | NM_001004416.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249048Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135192
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461378Hom.: 0 Cov.: 31 AF XY: 0.0000825 AC XY: 60AN XY: 727000
GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74454
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at