rs72973763
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001918.5(DBT):āc.715A>Gā(p.Ile239Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00595 in 1,613,626 control chromosomes in the GnomAD database, including 535 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I239L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001918.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DBT | NM_001918.5 | c.715A>G | p.Ile239Val | missense_variant | 6/11 | ENST00000370132.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBT | ENST00000370132.8 | c.715A>G | p.Ile239Val | missense_variant | 6/11 | 1 | NM_001918.5 | P1 | |
DBT | ENST00000370131.3 | c.715A>G | p.Ile239Val | missense_variant | 6/8 | 1 | |||
DBT | ENST00000681617.1 | c.715A>G | p.Ile239Val | missense_variant | 6/12 | ||||
DBT | ENST00000681780.1 | c.172A>G | p.Ile58Val | missense_variant | 7/12 |
Frequencies
GnomAD3 genomes ? AF: 0.0316 AC: 4804AN: 152096Hom.: 284 Cov.: 32
GnomAD3 exomes AF: 0.00833 AC: 2094AN: 251468Hom.: 110 AF XY: 0.00611 AC XY: 831AN XY: 135910
GnomAD4 exome AF: 0.00327 AC: 4780AN: 1461412Hom.: 252 Cov.: 30 AF XY: 0.00283 AC XY: 2056AN XY: 727060
GnomAD4 genome ? AF: 0.0316 AC: 4816AN: 152214Hom.: 283 Cov.: 32 AF XY: 0.0307 AC XY: 2286AN XY: 74428
ClinVar
Submissions by phenotype
Maple syrup urine disease Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 08, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 23, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at