3-69028258-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007114.3(TMF1):c.2632G>A(p.Val878Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007114.3 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 |
---|---|---|---|---|---|---|---|---|
TMF1 | NM_007114.3 | c.2632G>A | p.Val878Ile | missense_variant | Exon 12 of 17 | ENST00000398559.7 | NP_009045.2 | |
TMF1 | NM_001363879.1 | c.2641G>A | p.Val881Ile | missense_variant | Exon 12 of 17 | NP_001350808.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249120Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135210
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1460966Hom.: 0 Cov.: 29 AF XY: 0.0000275 AC XY: 20AN XY: 726872
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2632G>A (p.V878I) alteration is located in exon 12 (coding exon 12) of the TMF1 gene. This alteration results from a G to A substitution at nucleotide position 2632, causing the valine (V) at amino acid position 878 to be replaced by an isoleucine (I). 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