rs8923
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006441.4(MTHFS):āc.604A>Gā(p.Thr202Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0852 in 1,614,148 control chromosomes in the GnomAD database, including 6,373 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T202I) has been classified as Uncertain significance.
Frequency
Consequence
NM_006441.4 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 | UniProt |
---|---|---|---|---|---|---|---|
MTHFS | NM_006441.4 | c.604A>G | p.Thr202Ala | missense_variant | 3/3 | ENST00000258874.4 | |
ST20-MTHFS | NM_001199760.2 | c.532A>G | p.Thr178Ala | missense_variant | 4/4 | ||
MTHFS | NM_001199758.1 | c.433A>G | p.Thr145Ala | missense_variant | 3/3 | ||
MTHFS | NR_037654.2 | n.711A>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFS | ENST00000258874.4 | c.604A>G | p.Thr202Ala | missense_variant | 3/3 | 1 | NM_006441.4 | P1 | |
MTHFS | ENST00000559722.2 | c.691A>G | p.Thr231Ala | missense_variant | 3/3 | 2 | |||
MTHFS | ENST00000560261.1 | c.112A>G | p.Thr38Ala | missense_variant, NMD_transcript_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0746 AC: 11351AN: 152178Hom.: 478 Cov.: 32
GnomAD3 exomes AF: 0.0666 AC: 16739AN: 251310Hom.: 717 AF XY: 0.0674 AC XY: 9159AN XY: 135816
GnomAD4 exome AF: 0.0863 AC: 126177AN: 1461852Hom.: 5895 Cov.: 31 AF XY: 0.0848 AC XY: 61642AN XY: 727234
GnomAD4 genome ? AF: 0.0746 AC: 11358AN: 152296Hom.: 478 Cov.: 32 AF XY: 0.0712 AC XY: 5305AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at