1-11786602-ATTTT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_005957(MTHFR):c.*4074_*4077del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.54 ( 21344 hom., cov: 0)
Consequence
MTHFR
NM_005957 3_prime_UTR
NM_005957 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.308
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1:11786602-ATTTT>A is Benign according to our data. Variant chr1-11786602-ATTTT-A is described in ClinVar as [Likely_benign]. Clinvar id is 292164. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTHFR | NM_005957.5 | c.*4074_*4077del | 3_prime_UTR_variant | 12/12 | ENST00000376590.9 | ||
C1orf167 | NM_001010881.2 | c.3568-770_3568-767del | intron_variant | ENST00000688073.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFR | ENST00000376590.9 | c.*4074_*4077del | 3_prime_UTR_variant | 12/12 | 1 | NM_005957.5 | A1 | ||
C1orf167 | ENST00000688073.1 | c.3568-770_3568-767del | intron_variant | NM_001010881.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.542 AC: 76895AN: 141988Hom.: 21344 Cov.: 0
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GnomAD4 exome AF: 0.250 AC: 1AN: 4Hom.: 0 AC XY: 0AN XY: 0
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neural tube defects, folate-sensitive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at