chr12-109281736-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_213596.3(FOXN4):āc.965A>Gā(p.Glu322Gly) 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 1,454,890 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_213596.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXN4 | NM_213596.3 | c.965A>G | p.Glu322Gly | missense_variant | 9/10 | ENST00000299162.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXN4 | ENST00000299162.10 | c.965A>G | p.Glu322Gly | missense_variant | 9/10 | 1 | NM_213596.3 | P1 | |
FOXN4 | ENST00000423960.1 | c.*63A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 1 | ||||
FOXN4 | ENST00000355216.5 | c.425A>G | p.Glu142Gly | missense_variant | 5/6 | 2 | |||
FOXN4 | ENST00000468516.1 | c.143-2307A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240148Hom.: 0 AF XY: 0.00000763 AC XY: 1AN XY: 131064
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1454890Hom.: 0 Cov.: 31 AF XY: 0.00000277 AC XY: 2AN XY: 722906
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.965A>G (p.E322G) alteration is located in exon 9 (coding exon 8) of the FOXN4 gene. This alteration results from a A to G substitution at nucleotide position 965, causing the glutamic acid (E) at amino acid position 322 to be replaced by a glycine (G). 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