chr22-41382108-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003216.4(TEF):c.64C>T(p.Pro22Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000495 in 1,232,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P22T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEF | NM_003216.4 | c.64C>T | p.Pro22Ser | missense_variant | Exon 1 of 4 | ENST00000266304.9 | NP_003207.1 | |
TEF | NM_001145398.3 | c.68-5243C>T | intron_variant | Intron 1 of 3 | NP_001138870.1 | |||
LOC105373042 | XR_938271.3 | n.-197G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152098Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000481 AC: 52AN: 1080780Hom.: 0 Cov.: 33 AF XY: 0.0000431 AC XY: 22AN XY: 510278
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.64C>T (p.P22S) alteration is located in exon 1 (coding exon 1) of the TEF gene. This alteration results from a C to T substitution at nucleotide position 64, causing the proline (P) at amino acid position 22 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at