chr14-28767497-A-AGCCGCC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_005249.5(FOXG1):c.231_236dupGCCGCC(p.Pro78_Pro79dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 978,466 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005249.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXG1 | ENST00000313071.7 | c.231_236dupGCCGCC | p.Pro78_Pro79dup | disruptive_inframe_insertion | Exon 1 of 1 | 6 | NM_005249.5 | ENSP00000339004.3 | ||
FOXG1 | ENST00000706482.1 | c.231_236dupGCCGCC | p.Pro78_Pro79dup | disruptive_inframe_insertion | Exon 2 of 2 | ENSP00000516406.1 | ||||
LINC01551 | ENST00000675861.1 | n.374+1497_374+1502dupGCCGCC | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 5AN: 139878Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000334 AC: 28AN: 838492Hom.: 0 Cov.: 15 AF XY: 0.0000327 AC XY: 13AN XY: 398112
GnomAD4 genome AF: 0.0000357 AC: 5AN: 139974Hom.: 0 Cov.: 31 AF XY: 0.0000587 AC XY: 4AN XY: 68104
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed in large population cohorts (Lek et al., 2016); In-frame duplication in a repetitive region with no known function; Has not been previously published as pathogenic or benign to our knowledge -
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. -
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