chr1-11273983-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013319.3(UBIAD1):c.452A>G(p.Tyr151Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,614,056 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_013319.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBIAD1 | NM_013319.3 | c.452A>G | p.Tyr151Cys | missense_variant | 1/2 | ENST00000376810.6 | |
UBIAD1 | NM_001330349.2 | c.452A>G | p.Tyr151Cys | missense_variant | 1/3 | ||
UBIAD1 | NM_001330350.2 | c.452A>G | p.Tyr151Cys | missense_variant | 1/2 | ||
UBIAD1 | XM_047418727.1 | c.452A>G | p.Tyr151Cys | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBIAD1 | ENST00000376810.6 | c.452A>G | p.Tyr151Cys | missense_variant | 1/2 | 1 | NM_013319.3 | P1 | |
UBIAD1 | ENST00000376804.2 | c.452A>G | p.Tyr151Cys | missense_variant | 1/2 | 2 | |||
UBIAD1 | ENST00000483738.1 | c.50A>G | p.Tyr17Cys | missense_variant | 1/3 | 3 | |||
UBIAD1 | ENST00000486588.6 | c.95A>G | p.Tyr32Cys | missense_variant, NMD_transcript_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00157 AC: 238AN: 152054Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000380 AC: 95AN: 250028Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135284
GnomAD4 exome AF: 0.000136 AC: 199AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 727244
GnomAD4 genome ? AF: 0.00156 AC: 238AN: 152172Hom.: 2 Cov.: 32 AF XY: 0.00169 AC XY: 126AN XY: 74392
ClinVar
Submissions by phenotype
UBIAD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 31, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 23, 2022 | - - |
Schnyder crystalline corneal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at