rs751474426
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM2PP3BP6BS1
The NM_175748.4(UBR7):c.293G>A(p.Arg98His) variant causes a missense change. The variant allele was found at a frequency of 0.0000081 in 1,605,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000076 ( 0 hom. )
Consequence
UBR7
NM_175748.4 missense
NM_175748.4 missense
Scores
6
7
3
Clinical Significance
Conservation
PhyloP100: 5.98
Genes affected
UBR7 (HGNC:20344): (ubiquitin protein ligase E3 component n-recognin 7) This gene encodes a UBR box-containing protein that belongs to the E3 ubiquitin ligase family. The protein also contains a plant homeodomain (PHD) in the C-terminus. In mammals, the encoded protein recognizes N-degrons, the destabilizing N-terminal residues of short-lived proteins, which results in ubiquitinylation, and proteolysis via the proteasome. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.782
BP6
?
Variant 14-93210656-G-A is Benign according to our data. Variant chr14-93210656-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 207868.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00000757 (11/1453936) while in subpopulation AMR AF= 0.0000684 (3/43870). AF 95% confidence interval is 0.0000181. There are 0 homozygotes in gnomad4_exome. There are 6 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBR7 | NM_175748.4 | c.293G>A | p.Arg98His | missense_variant | 3/11 | ENST00000013070.11 | |
UBR7 | NR_038150.2 | n.195G>A | non_coding_transcript_exon_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBR7 | ENST00000013070.11 | c.293G>A | p.Arg98His | missense_variant | 3/11 | 1 | NM_175748.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000832 AC: 2AN: 240496Hom.: 0 AF XY: 0.00000770 AC XY: 1AN XY: 129914
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GnomAD4 exome AF: 0.00000757 AC: 11AN: 1453936Hom.: 0 Cov.: 30 AF XY: 0.00000830 AC XY: 6AN XY: 722696
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74216
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Benign
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
1.0
.;D;.
Vest4
0.38
MutPred
0.63
.;Loss of MoRF binding (P = 0.0453);Loss of MoRF binding (P = 0.0453);
MVP
MPC
0.63
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at