chr9-97854739-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004473.4(FOXE1):c.825C>T(p.Ser275=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 1,456,554 control chromosomes in the GnomAD database, including 282,582 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.63 ( 30736 hom., cov: 34)
Exomes 𝑓: 0.62 ( 251846 hom. )
Consequence
FOXE1
NM_004473.4 synonymous
NM_004473.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.67
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 9-97854739-C-T is Benign according to our data. Variant chr9-97854739-C-T is described in ClinVar as [Benign]. Clinvar id is 95098.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-97854739-C-T is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-2.67 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXE1 | NM_004473.4 | c.825C>T | p.Ser275= | synonymous_variant | 1/1 | ENST00000375123.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXE1 | ENST00000375123.5 | c.825C>T | p.Ser275= | synonymous_variant | 1/1 | NM_004473.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.633 AC: 96098AN: 151754Hom.: 30711 Cov.: 34
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GnomAD3 exomes AF: 0.672 AC: 40853AN: 60772Hom.: 13965 AF XY: 0.667 AC XY: 22521AN XY: 33768
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GnomAD4 exome AF: 0.619 AC: 807716AN: 1304692Hom.: 251846 Cov.: 57 AF XY: 0.619 AC XY: 395965AN XY: 639986
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GnomAD4 genome AF: 0.633 AC: 96157AN: 151862Hom.: 30736 Cov.: 34 AF XY: 0.638 AC XY: 47349AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 22, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Bamforth-Lazarus syndrome Benign:1
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at