chr14-93210703-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_175748.4(UBR7):c.340C>T(p.Leu114Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,608,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_175748.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBR7 | ENST00000013070.11 | c.340C>T | p.Leu114Phe | missense_variant | Exon 3 of 11 | 1 | NM_175748.4 | ENSP00000013070.6 | ||
ENSG00000259066 | ENST00000557574.1 | c.397C>T | p.Leu133Phe | missense_variant | Exon 4 of 5 | 4 | ENSP00000451369.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 243682Hom.: 0 AF XY: 0.00000760 AC XY: 1AN XY: 131622
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1456092Hom.: 0 Cov.: 30 AF XY: 0.0000111 AC XY: 8AN XY: 723958
GnomAD4 genome AF: 0.000118 AC: 18AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:1
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