chr20-22581844-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_021784.5(FOXA2):c.*6C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 1,607,094 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021784.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXA2 | NM_021784.5 | c.*6C>T | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000419308.7 | NP_068556.2 | ||
FOXA2 | NM_153675.3 | c.*6C>T | 3_prime_UTR_variant | Exon 3 of 3 | NP_710141.1 | |||
FOXA2 | XM_047440133.1 | c.*6C>T | 3_prime_UTR_variant | Exon 3 of 3 | XP_047296089.1 | |||
FOXA2 | XM_047440134.1 | c.*6C>T | 3_prime_UTR_variant | Exon 2 of 2 | XP_047296090.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00206 AC: 314AN: 152126Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00183 AC: 456AN: 249286Hom.: 2 AF XY: 0.00189 AC XY: 255AN XY: 135276
GnomAD4 exome AF: 0.00328 AC: 4770AN: 1454850Hom.: 8 Cov.: 29 AF XY: 0.00311 AC XY: 2249AN XY: 722346
GnomAD4 genome AF: 0.00206 AC: 313AN: 152244Hom.: 1 Cov.: 32 AF XY: 0.00200 AC XY: 149AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:1
- -
FOXA2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
FOXA2: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at