14-64449447-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005956.4(MTHFD1):c.2282C>T(p.Thr761Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00633 in 1,613,056 control chromosomes in the GnomAD database, including 362 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Synonymous variant affecting the same amino acid position (i.e. T761T) has been classified as Likely benign.
Frequency
Consequence
NM_005956.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTHFD1 | NM_005956.4 | c.2282C>T | p.Thr761Met | missense_variant, splice_region_variant | Exon 24 of 28 | ENST00000652337.1 | NP_005947.3 | |
MTHFD1 | NM_001364837.1 | c.2282C>T | p.Thr761Met | missense_variant, splice_region_variant | Exon 24 of 27 | NP_001351766.1 | ||
ZBTB25 | NM_001304508.1 | c.*104G>A | 3_prime_UTR_variant | Exon 3 of 3 | NP_001291437.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0261 AC: 3973AN: 152152Hom.: 151 Cov.: 32
GnomAD3 exomes AF: 0.00987 AC: 2478AN: 251140Hom.: 83 AF XY: 0.00882 AC XY: 1198AN XY: 135766
GnomAD4 exome AF: 0.00427 AC: 6233AN: 1460786Hom.: 210 Cov.: 30 AF XY: 0.00451 AC XY: 3280AN XY: 726696
GnomAD4 genome AF: 0.0262 AC: 3984AN: 152270Hom.: 152 Cov.: 32 AF XY: 0.0255 AC XY: 1901AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at