1-11790673-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005957(MTHFR):c.*7G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000723 in 152130 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
MTHFR
NM_005957 3_prime_UTR
NM_005957 3_prime_UTR
Scores
6
Clinical Significance
Conservation
PhyloP100: -5.27
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010073274).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTHFR | NM_005957.5 | c.*7G>A | 3_prime_UTR_variant | 12/12 | ENST00000376590.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFR | ENST00000376590.9 | c.*7G>A | 3_prime_UTR_variant | 12/12 | 1 | NM_005957.5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152130Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000159 AC: 40AN: 250858Hom.: 1 AF XY: 0.000229 AC XY: 31AN XY: 135602
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GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461560Hom.: 3 AF XY: 0.000116 AC XY: 84AN XY: 727050
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 29, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
N;N;N;N
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at