1-11790683-T-C
Variant summary
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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000040 ( 0 hom. )
Consequence
MTHFR
NM_005957 synonymous
NM_005957 synonymous
Scores
6
Clinical Significance
Conservation
PhyloP100: -2.22
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.00000658 (1/152054) while in subpopulation AFR AF= 0.0000242 (1/41394). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 1 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.070465684).
BP6
?
Variant 1:11790683-T>C is Benign according to our data. Variant chr1-11790683-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1087028. Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.22 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTHFR | NM_005957.5 | c.1968A>G | p.Pro656= | synonymous_variant | 12/12 | ENST00000376590.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFR | ENST00000376590.9 | c.1968A>G | p.Pro656= | synonymous_variant | 12/12 | 1 | NM_005957.5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251238Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135792
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Homocystinuria due to methylene tetrahydrofolate reductase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 13, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
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T
MutationTaster
Benign
N;N;N;N
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at