rs2115540
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001199760.2(ST20-MTHFS):c.46-8612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,016 control chromosomes in the GnomAD database, including 17,898 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.47 ( 17898 hom., cov: 32)
Consequence
ST20-MTHFS
NM_001199760.2 intron
NM_001199760.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0840
Genes affected
ST20-MTHFS (HGNC:44655): (ST20-MTHFS readthrough) This locus represents naturally occurring read-through transcription between the neighboring suppressor of tumorigenicity 20 and 5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase) genes on chromosome 15. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST20-MTHFS | NM_001199760.2 | c.46-8612T>C | intron_variant | NP_001186689.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST20-MTHFS | ENST00000479961.1 | c.46-8612T>C | intron_variant | 3 | ENSP00000455643.1 | |||||
ST20-MTHFS | ENST00000615374.5 | c.46-8612T>C | intron_variant | 3 | ENSP00000489525.1 | |||||
ST20-MTHFS | ENST00000494999.1 | c.40-8612T>C | intron_variant | 3 | ENSP00000489298.1 |
Frequencies
GnomAD3 genomes AF: 0.474 AC: 71973AN: 151898Hom.: 17882 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.474 AC: 72025AN: 152016Hom.: 17898 Cov.: 32 AF XY: 0.469 AC XY: 34824AN XY: 74282
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at