1-236795531-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000254.3(MTR):c.-173G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000469 in 1,530,536 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000254.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00113 AC: 160AN: 141910Hom.: 1 AF XY: 0.00152 AC XY: 117AN XY: 77192
GnomAD4 exome AF: 0.000492 AC: 678AN: 1378190Hom.: 7 Cov.: 31 AF XY: 0.000692 AC XY: 471AN XY: 680514
GnomAD4 genome AF: 0.000263 AC: 40AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74488
ClinVar
Submissions by phenotype
Disorders of Intracellular Cobalamin Metabolism Benign:1
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at