rs2273028
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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.815-23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,522,650 control chromosomes in the GnomAD database, including 80,193 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 0.36 ( 10871 hom., cov: 32)
Exomes 𝑓: 0.31 ( 69322 hom. )
Consequence
SHMT1
NM_004169.5 intron
NM_004169.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.390
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHMT1 | NM_004169.5 | c.815-23C>T | intron_variant | ENST00000316694.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHMT1 | ENST00000316694.8 | c.815-23C>T | intron_variant | 1 | NM_004169.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.361 AC: 54778AN: 151882Hom.: 10852 Cov.: 32
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GnomAD3 exomes AF: 0.294 AC: 73951AN: 251470Hom.: 12033 AF XY: 0.288 AC XY: 39161AN XY: 135914
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GnomAD4 exome AF: 0.311 AC: 426193AN: 1370650Hom.: 69322 Cov.: 21 AF XY: 0.307 AC XY: 210720AN XY: 687012
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GnomAD4 genome ? AF: 0.361 AC: 54853AN: 152000Hom.: 10871 Cov.: 32 AF XY: 0.355 AC XY: 26393AN XY: 74290
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at