chr20-22582241-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_021784.5(FOXA2):c.1001C>T(p.Ala334Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000665 in 1,473,698 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_021784.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXA2 | NM_021784.5 | c.1001C>T | p.Ala334Val | missense_variant | 2/2 | ENST00000419308.7 | |
FOXA2 | NM_153675.3 | c.983C>T | p.Ala328Val | missense_variant | 3/3 | ||
FOXA2 | XM_047440133.1 | c.983C>T | p.Ala328Val | missense_variant | 3/3 | ||
FOXA2 | XM_047440134.1 | c.893C>T | p.Ala298Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXA2 | ENST00000419308.7 | c.1001C>T | p.Ala334Val | missense_variant | 2/2 | 1 | NM_021784.5 | P4 | |
FOXA2 | ENST00000377115.4 | c.983C>T | p.Ala328Val | missense_variant | 3/3 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152092Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000244 AC: 18AN: 73716Hom.: 0 AF XY: 0.000253 AC XY: 10AN XY: 39574
GnomAD4 exome AF: 0.0000621 AC: 82AN: 1321498Hom.: 0 Cov.: 35 AF XY: 0.0000617 AC XY: 40AN XY: 647996
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at