Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM2_SupportingBP4_ModerateBP6_ModerateBP7
The NM_005957(MTHFR):c.1968A>G(p.Pro656=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152054 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Verdict is Likely_benign. Variant got -4 ACMG points.
GnomAD3 genomes AF: 0.00000658AC: 1AN: 152054Hom.: 0Cov.: 33 GnomAD3 exomes AF: 0.00000398AC: 1AN: 251238Hom.: 0 AF XY: 0.00000736AC XY: 1AN XY: 135792 GnomAD4 exome AF: 0.00000479AC: 7AN: 1461800Hom.: 0 AF XY: 0.00000825AC XY: 6AN XY: 727184
Submissions by phenotype
Homocystinuria due to methylene tetrahydrofolate reductase deficiency
|Likely benign, criteria provided, single submitter||clinical testing||Invitae||Mar 13, 2022||- -|
Find out detailed SpliceAI scores and Pangolin per-transcript scores at