14-28767485-CGCAGCA-CGCAGCAGCA
Variant names:
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The ENST00000313071.7(FOXG1):c.218_220dupAGC(p.Gln73dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000225 in 1,055,136 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★★★). Synonymous variant affecting the same amino acid position (i.e. P74P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.00031 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
FOXG1
ENST00000313071.7 disruptive_inframe_insertion
ENST00000313071.7 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.214
Publications
1 publications found
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 was made for transcript
Our verdict: Benign. The variant received -13 ACMG points.
BP3
Nonframeshift variant in repetitive region in ENST00000313071.7
BP6
Variant 14-28767485-C-CGCA is Benign according to our data. Variant chr14-28767485-C-CGCA is described in ClinVar as Benign. ClinVar VariationId is 95265.Status of the report is reviewed_by_expert_panel, 3 stars.
BS2
High AC in GnomAd4 at 44 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000313071.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FOXG1 | NM_005249.5 | MANE Select | c.218_220dupAGC | p.Gln73dup | disruptive_inframe_insertion | Exon 1 of 1 | NP_005240.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FOXG1 | ENST00000313071.7 | TSL:6 MANE Select | c.218_220dupAGC | p.Gln73dup | disruptive_inframe_insertion | Exon 1 of 1 | ENSP00000339004.3 | ||
| FOXG1 | ENST00000706482.1 | c.218_220dupAGC | p.Gln73dup | disruptive_inframe_insertion | Exon 2 of 2 | ENSP00000516406.1 | |||
| LINC01551 | ENST00000675861.1 | n.374+1484_374+1486dupAGC | intron | N/A |
Frequencies
GnomAD3 genomes 0.000306 AC: 44AN: 143906Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
44
AN:
143906
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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AF:
Gnomad FIN
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000318 AC: 2AN: 62992 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
62992
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.000212 AC: 193AN: 911142Hom.: 0 Cov.: 16 AF XY: 0.000241 AC XY: 106AN XY: 440340 show subpopulations
GnomAD4 exome
AF:
AC:
193
AN:
911142
Hom.:
Cov.:
16
AF XY:
AC XY:
106
AN XY:
440340
show subpopulations
African (AFR)
AF:
AC:
1
AN:
18250
American (AMR)
AF:
AC:
1
AN:
16728
Ashkenazi Jewish (ASJ)
AF:
AC:
14
AN:
11830
East Asian (EAS)
AF:
AC:
1
AN:
11310
South Asian (SAS)
AF:
AC:
3
AN:
33370
European-Finnish (FIN)
AF:
AC:
0
AN:
13704
Middle Eastern (MID)
AF:
AC:
3
AN:
2174
European-Non Finnish (NFE)
AF:
AC:
164
AN:
771534
Other (OTH)
AF:
AC:
6
AN:
32242
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.470
Heterozygous variant carriers
0
9
19
28
38
47
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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10
20
30
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<30
30-35
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>80
Age
GnomAD4 genome 0.000306 AC: 44AN: 143994Hom.: 0 Cov.: 31 AF XY: 0.000328 AC XY: 23AN XY: 70064 show subpopulations
GnomAD4 genome
AF:
AC:
44
AN:
143994
Hom.:
Cov.:
31
AF XY:
AC XY:
23
AN XY:
70064
show subpopulations
African (AFR)
AF:
AC:
9
AN:
39870
American (AMR)
AF:
AC:
1
AN:
14578
Ashkenazi Jewish (ASJ)
AF:
AC:
9
AN:
3322
East Asian (EAS)
AF:
AC:
1
AN:
4932
South Asian (SAS)
AF:
AC:
2
AN:
4662
European-Finnish (FIN)
AF:
AC:
0
AN:
8304
Middle Eastern (MID)
AF:
AC:
0
AN:
270
European-Non Finnish (NFE)
AF:
AC:
22
AN:
65178
Other (OTH)
AF:
AC:
0
AN:
1984
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
3
5
8
10
13
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
Significance:Benign
Revision:reviewed by expert panel
Pathogenic
VUS
Benign
Condition
-
1
1
not provided (2)
-
-
2
Rett syndrome, congenital variant (2)
-
-
1
FOXG1 disorder (1)
-
-
1
FOXG1-related disorder (1)
-
-
1
Inborn genetic diseases (1)
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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