chr12-123253386-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152269.5(MTRFR):c.-28-261G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 398,792 control chromosomes in the GnomAD database, including 1,927 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_152269.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0734 AC: 11125AN: 151608Hom.: 645 Cov.: 30
GnomAD4 exome AF: 0.0848 AC: 20961AN: 247066Hom.: 1282 Cov.: 2 AF XY: 0.0777 AC XY: 10388AN XY: 133648
GnomAD4 genome AF: 0.0733 AC: 11127AN: 151726Hom.: 645 Cov.: 30 AF XY: 0.0709 AC XY: 5255AN XY: 74106
ClinVar
Submissions by phenotype
not provided Benign:2
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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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at