chr6-41587430-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012426.2(FOXP4):c.790G>A(p.Ala264Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 1,575,054 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_001012426.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP4 | NM_001012426.2 | c.790G>A | p.Ala264Thr | missense_variant | 7/17 | ENST00000307972.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP4 | ENST00000307972.10 | c.790G>A | p.Ala264Thr | missense_variant | 7/17 | 1 | NM_001012426.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000188 AC: 4AN: 213006Hom.: 0 AF XY: 0.0000177 AC XY: 2AN XY: 112990
GnomAD4 exome AF: 0.0000112 AC: 16AN: 1422952Hom.: 0 Cov.: 34 AF XY: 0.00000995 AC XY: 7AN XY: 703622
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.790G>A (p.A264T) alteration is located in exon 7 (coding exon 6) of the FOXP4 gene. This alteration results from a G to A substitution at nucleotide position 790, causing the alanine (A) at amino acid position 264 to be replaced by a threonine (T). 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