chr3-69029869-G-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007114.3(TMF1):c.2540C>T(p.Ala847Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 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. A847T) has been classified as Uncertain significance.
Frequency
Consequence
NM_007114.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMF1 | NM_007114.3 | c.2540C>T | p.Ala847Val | missense_variant | Exon 11 of 17 | ENST00000398559.7 | NP_009045.2 | |
TMF1 | NM_001363879.1 | c.2549C>T | p.Ala850Val | missense_variant | Exon 11 of 17 | NP_001350808.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461614Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727118 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2540C>T (p.A847V) alteration is located in exon 11 (coding exon 11) of the TMF1 gene. This alteration results from a C to T substitution at nucleotide position 2540, causing the alanine (A) at amino acid position 847 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