rs1979277
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004169.5(SHMT1):c.1420C>T(p.Leu474Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,594,198 control chromosomes in the GnomAD database, including 74,438 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L474R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004169.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHMT1 | NM_004169.5 | c.1420C>T | p.Leu474Phe | missense_variant | 12/12 | ENST00000316694.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHMT1 | ENST00000316694.8 | c.1420C>T | p.Leu474Phe | missense_variant | 12/12 | 1 | NM_004169.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 46364AN: 151908Hom.: 7394 Cov.: 32
GnomAD3 exomes AF: 0.268 AC: 58787AN: 219198Hom.: 8365 AF XY: 0.265 AC XY: 31436AN XY: 118586
GnomAD4 exome AF: 0.300 AC: 432575AN: 1442172Hom.: 67041 Cov.: 38 AF XY: 0.296 AC XY: 211726AN XY: 715842
GnomAD4 genome AF: 0.305 AC: 46403AN: 152026Hom.: 7397 Cov.: 32 AF XY: 0.300 AC XY: 22326AN XY: 74318
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Uncertain:1
Uncertain significance, no assertion criteria provided | case-control | Department of Pharmacy and Biotechnology, University of Bologna | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at