rs542787885
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005249.5(FOXG1):c.-216_-210delTTTTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FOXG1
NM_005249.5 5_prime_UTR
NM_005249.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.983
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXG1 | ENST00000313071 | c.-216_-210delTTTTTTT | 5_prime_UTR_variant | Exon 1 of 1 | NM_005249.5 | ENSP00000339004.3 | ||||
FOXG1 | ENST00000706482 | c.-216_-210delTTTTTTT | 5_prime_UTR_variant | Exon 2 of 2 | ENSP00000516406.1 | |||||
LINC01551 | ENST00000675861.1 | n.374+1051_374+1057delTTTTTTT | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD3 genomes
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 3454Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 1978
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
3454
Hom.:
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AC XY:
0
AN XY:
1978
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GnomAD4 genome Cov.: 29
GnomAD4 genome
Cov.:
29
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at