NM_005249.5:c.1384A>G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP5BA1
This summary comes from the ClinGen Evidence Repository: The allele frequency of the p.Ser462Gly variant in FOXG1 is 0.147% in South Asian sub population in gnomAD v2, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The Ser462Gly variant is found in a patient with an alternate molecular basis of disease (internal database - Invitae) (BP5). In summary, the p.Ser462Gly variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BP5). LINK:https://erepo.genome.network/evrepo/ui/classification/CA208363/MONDO:0100040/035
Frequency
Consequence
NM_005249.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXG1 | ENST00000313071.7 | c.1384A>G | p.Ser462Gly | missense_variant | Exon 1 of 1 | 6 | NM_005249.5 | ENSP00000339004.3 | ||
FOXG1 | ENST00000706482.1 | c.1384A>G | p.Ser462Gly | missense_variant | Exon 2 of 2 | ENSP00000516406.1 | ||||
LINC01551 | ENST00000675861.1 | n.374+2650A>G | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251490Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135920
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461894Hom.: 1 Cov.: 34 AF XY: 0.000133 AC XY: 97AN XY: 727248
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
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not provided Benign:1
FOXG1: PP2, BS1 -
FOXG1 disorder Benign:1
The allele frequency of the p.Ser462Gly variant in FOXG1 is 0.147% in South Asian sub population in gnomAD v2, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The Ser462Gly variant is found in a patient with an alternate molecular basis of disease (internal database - Invitae) (BP5). In summary, the p.Ser462Gly variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BP5). -
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