NM_021784.5:c.855A>G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_021784.5(FOXA2):āc.855A>Gā(p.Gly285Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 1,541,352 control chromosomes in the GnomAD database, including 10,394 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_021784.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXA2 | NM_021784.5 | c.855A>G | p.Gly285Gly | synonymous_variant | Exon 2 of 2 | ENST00000419308.7 | NP_068556.2 | |
FOXA2 | NM_153675.3 | c.837A>G | p.Gly279Gly | synonymous_variant | Exon 3 of 3 | NP_710141.1 | ||
FOXA2 | XM_047440133.1 | c.837A>G | p.Gly279Gly | synonymous_variant | Exon 3 of 3 | XP_047296089.1 | ||
FOXA2 | XM_047440134.1 | c.747A>G | p.Gly249Gly | synonymous_variant | Exon 2 of 2 | XP_047296090.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXA2 | ENST00000419308.7 | c.855A>G | p.Gly285Gly | synonymous_variant | Exon 2 of 2 | 1 | NM_021784.5 | ENSP00000400341.3 | ||
FOXA2 | ENST00000377115.4 | c.837A>G | p.Gly279Gly | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000366319.4 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 25115AN: 152050Hom.: 4567 Cov.: 33
GnomAD3 exomes AF: 0.0869 AC: 13607AN: 156562Hom.: 1406 AF XY: 0.0828 AC XY: 7126AN XY: 86062
GnomAD4 exome AF: 0.0577 AC: 80181AN: 1389188Hom.: 5790 Cov.: 35 AF XY: 0.0584 AC XY: 40049AN XY: 685574
GnomAD4 genome AF: 0.166 AC: 25199AN: 152164Hom.: 4604 Cov.: 33 AF XY: 0.163 AC XY: 12099AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:2
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FOXA2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at