22-41382121-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.77C>T(p.Ala26Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,234,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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.77C>T | p.Ala26Val | missense_variant | Exon 1 of 4 | ENST00000266304.9 | NP_003207.1 | |
TEF | NM_001145398.3 | c.68-5230C>T | intron_variant | Intron 1 of 3 | NP_001138870.1 | |||
LOC105373042 | XR_938271.3 | n.-210G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151754Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000554 AC: 60AN: 1082736Hom.: 0 Cov.: 32 AF XY: 0.0000704 AC XY: 36AN XY: 511462
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151754Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74122
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.77C>T (p.A26V) 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 77, causing the alanine (A) at amino acid position 26 to be replaced by a valine (V). 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