1-236795360-C-T
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_000254.3(MTR):c.-344C>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 0.00102 in 1,358,146 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000254.3 5_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- methylcobalamin deficiency type cblGInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Benign. The variant received -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152224Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000706 AC: 88AN: 124600 AF XY: 0.000765 show subpopulations
GnomAD4 exome AF: 0.00108 AC: 1299AN: 1205804Hom.: 5 Cov.: 30 AF XY: 0.00110 AC XY: 651AN XY: 590370 show subpopulations
GnomAD4 genome AF: 0.000545 AC: 83AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74498 show subpopulations
ClinVar
Submissions by phenotype
Disorders of Intracellular Cobalamin Metabolism Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at