chr20-22582123-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_021784.5(FOXA2):c.1119A>C(p.Glu373Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,596,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E373V) has been classified as Uncertain significance.
Frequency
Consequence
NM_021784.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXA2 | NM_021784.5 | c.1119A>C | p.Glu373Asp | missense_variant | 2/2 | ENST00000419308.7 | |
FOXA2 | NM_153675.3 | c.1101A>C | p.Glu367Asp | missense_variant | 3/3 | ||
FOXA2 | XM_047440133.1 | c.1101A>C | p.Glu367Asp | missense_variant | 3/3 | ||
FOXA2 | XM_047440134.1 | c.1011A>C | p.Glu337Asp | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXA2 | ENST00000419308.7 | c.1119A>C | p.Glu373Asp | missense_variant | 2/2 | 1 | NM_021784.5 | P4 | |
FOXA2 | ENST00000377115.4 | c.1101A>C | p.Glu367Asp | missense_variant | 3/3 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 6AN: 213342Hom.: 0 AF XY: 0.0000174 AC XY: 2AN XY: 115194
GnomAD4 exome AF: 0.00000761 AC: 11AN: 1444594Hom.: 0 Cov.: 35 AF XY: 0.00000837 AC XY: 6AN XY: 717034
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at