rs12952556
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004169.5(SHMT1):c.*267A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 496,084 control chromosomes in the GnomAD database, including 21,454 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 0.31 ( 7577 hom., cov: 33)
Exomes 𝑓: 0.27 ( 13877 hom. )
Consequence
SHMT1
NM_004169.5 3_prime_UTR
NM_004169.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.96
Genes affected
SHMT1 (HGNC:10850): (serine hydroxymethyltransferase 1) This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHMT1 | NM_004169.5 | c.*267A>G | 3_prime_UTR_variant | 12/12 | ENST00000316694.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHMT1 | ENST00000316694.8 | c.*267A>G | 3_prime_UTR_variant | 12/12 | 1 | NM_004169.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.308 AC: 46855AN: 152028Hom.: 7574 Cov.: 33
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GnomAD4 exome AF: 0.273 AC: 93805AN: 343938Hom.: 13877 Cov.: 3 AF XY: 0.266 AC XY: 48321AN XY: 181488
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GnomAD4 genome ? AF: 0.308 AC: 46895AN: 152146Hom.: 7577 Cov.: 33 AF XY: 0.303 AC XY: 22567AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at