chr14-28767441-T-TCAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong
The NM_005249.5(FOXG1):c.170_172dup(p.His57dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000408 in 1,176,016 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. H54H) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000078 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000045 ( 0 hom. )
Consequence
FOXG1
NM_005249.5 inframe_insertion
NM_005249.5 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
FOXG1 (HGNC:3811): (forkhead box G1) This locus encodes a member of the fork-head transcription factor family. The encoded protein, which functions as a transcriptional repressor, is highly expressed in neural tissues during brain development. Mutations at this locus have been associated with Rett syndrome and a diverse spectrum of neurodevelopmental disorders defined as part of the FOXG1 syndrome. This gene is disregulated in many types of cancer and is the target of multiple microRNAs that regulate the proliferation of tumor cells. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP6
?
Variant 14-28767441-T-TCAC is Benign according to our data. Variant chr14-28767441-T-TCAC is described in ClinVar as [Likely_benign]. Clinvar id is 487209.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXG1 | NM_005249.5 | c.170_172dup | p.His57dup | inframe_insertion | 1/1 | ENST00000313071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXG1 | ENST00000313071.7 | c.170_172dup | p.His57dup | inframe_insertion | 1/1 | NM_005249.5 | P1 | ||
FOXG1 | ENST00000706482.1 | c.170_172dup | p.His57dup | inframe_insertion | 2/2 | P1 | |||
LINC01551 | ENST00000675861.1 | n.374+1436_374+1438dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000779 AC: 1AN: 128424Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000449 AC: 47AN: 1047592Hom.: 0 Cov.: 24 AF XY: 0.0000408 AC XY: 21AN XY: 515044
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | FOXG1: BP3 - |
Rett syndrome, congenital variant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at