12-51098907-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005653.5(TFCP2):āc.1288A>Cā(p.Ile430Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005653.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFCP2 | NM_005653.5 | c.1288A>C | p.Ile430Leu | missense_variant | 13/15 | ENST00000257915.10 | |
TFCP2 | NM_001173452.2 | c.1288A>C | p.Ile430Leu | missense_variant | 13/15 | ||
TFCP2 | NM_001173453.2 | c.1135A>C | p.Ile379Leu | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFCP2 | ENST00000257915.10 | c.1288A>C | p.Ile430Leu | missense_variant | 13/15 | 1 | NM_005653.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251308Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135826
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727218
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.1288A>C (p.I430L) alteration is located in exon 13 (coding exon 13) of the TFCP2 gene. This alteration results from a A to C substitution at nucleotide position 1288, causing the isoleucine (I) at amino acid position 430 to be replaced by a leucine (L). 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