rs200947520
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005957.5(MTHFR):c.1932C>A(p.Asn644Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,614,246 control chromosomes in the GnomAD database, including 5 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_005957.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTHFR | NM_005957.5 | c.1932C>A | p.Asn644Lys | missense_variant | 12/12 | ENST00000376590.9 | NP_005948.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTHFR | ENST00000376590.9 | c.1932C>A | p.Asn644Lys | missense_variant | 12/12 | 1 | NM_005957.5 | ENSP00000365775.3 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000453 AC: 114AN: 251402Hom.: 2 AF XY: 0.000640 AC XY: 87AN XY: 135868
GnomAD4 exome AF: 0.000196 AC: 287AN: 1461888Hom.: 5 Cov.: 31 AF XY: 0.000294 AC XY: 214AN XY: 727244
GnomAD4 genome AF: 0.000112 AC: 17AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74518
ClinVar
Submissions by phenotype
MTHFR-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 25, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Homocystinuria due to methylene tetrahydrofolate reductase deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at