rs1867278
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004473.4(FOXE1):c.-248C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 359,054 control chromosomes in the GnomAD database, including 72,582 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.63 ( 30761 hom., cov: 32)
Exomes 𝑓: 0.63 ( 41821 hom. )
Consequence
FOXE1
NM_004473.4 5_prime_UTR
NM_004473.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.416
Genes affected
FOXE1 (HGNC:3806): (forkhead box E1) This intronless gene encodes a protein that belongs to the forkhead family of transcription factors. Members of this family contain a conserved 100-amino acid DNA-binding 'forkhead' domain. The encoded protein functions as a thyroid transcription factor that plays a role in thyroid morphogenesis. Mutations in this gene are associated with the Bamforth-Lazarus syndrome, and with susceptibility to nonmedullary thyroid cancer-4. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 9-97853667-C-A is Benign according to our data. Variant chr9-97853667-C-A is described in ClinVar as [Benign]. Clinvar id is 1253567.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXE1 | NM_004473.4 | c.-248C>A | 5_prime_UTR_variant | 1/1 | ENST00000375123.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXE1 | ENST00000375123.5 | c.-248C>A | 5_prime_UTR_variant | 1/1 | NM_004473.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.633 AC: 96190AN: 151916Hom.: 30734 Cov.: 32
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GnomAD4 exome AF: 0.630 AC: 130329AN: 207022Hom.: 41821 Cov.: 3 AF XY: 0.626 AC XY: 66295AN XY: 105864
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GnomAD4 genome ? AF: 0.633 AC: 96253AN: 152032Hom.: 30761 Cov.: 32 AF XY: 0.638 AC XY: 47380AN XY: 74320
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at