9-97854397-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004473.4(FOXE1):c.483G>C(p.Met161Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000127 in 1,338,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004473.4 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 |
---|---|---|---|---|---|---|---|
FOXE1 | NM_004473.4 | c.483G>C | p.Met161Ile | missense_variant | 1/1 | ENST00000375123.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXE1 | ENST00000375123.5 | c.483G>C | p.Met161Ile | missense_variant | 1/1 | NM_004473.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000144 AC: 2AN: 139008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000188 AC: 2AN: 106318Hom.: 0 AF XY: 0.0000159 AC XY: 1AN XY: 62822
GnomAD4 exome AF: 0.0000125 AC: 15AN: 1199512Hom.: 0 Cov.: 51 AF XY: 0.0000169 AC XY: 10AN XY: 590332
GnomAD4 genome ? AF: 0.0000144 AC: 2AN: 139008Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 67296
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.483G>C (p.M161I) alteration is located in exon 1 (coding exon 1) of the FOXE1 gene. This alteration results from a G to C substitution at nucleotide position 483, causing the methionine (M) at amino acid position 161 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