14-28767497-AGCCGCCGCC-AGCCGCC
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_005249.5(FOXG1):c.234_236delGCC(p.Pro79del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000329 in 975,818 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005249.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXG1 | ENST00000313071.7 | c.234_236delGCC | p.Pro79del | disruptive_inframe_deletion | Exon 1 of 1 | 6 | NM_005249.5 | ENSP00000339004.3 | ||
FOXG1 | ENST00000706482.1 | c.234_236delGCC | p.Pro79del | disruptive_inframe_deletion | Exon 2 of 2 | ENSP00000516406.1 | ||||
LINC01551 | ENST00000675861.1 | n.374+1500_374+1502delGCC | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000572 AC: 8AN: 139876Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.000374 AC: 313AN: 835846Hom.: 0 AF XY: 0.000413 AC XY: 164AN XY: 396838
GnomAD4 genome AF: 0.0000572 AC: 8AN: 139972Hom.: 0 Cov.: 31 AF XY: 0.0000294 AC XY: 2AN XY: 68102
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
FOXG1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Rett syndrome, congenital variant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at