chrX-54455400-C-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004463.3(FGD1):c.2015+48G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,023,584 control chromosomes in the GnomAD database, including 27,486 homozygotes. There are 61,737 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.37 ( 9193 hom., 11931 hem., cov: 23)
Exomes 𝑓: 0.19 ( 18293 hom. 49806 hem. )
Consequence
FGD1
NM_004463.3 intron
NM_004463.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.141
Genes affected
FGD1 (HGNC:3663): (FYVE, RhoGEF and PH domain containing 1) This gene encodes a protein that contains Dbl (DH) and pleckstrin (PH) homology domains and is similar to the Rho family of small GTP-binding proteins. The encoded protein specifically binds to the Rho family GTPase Cdc42Hs and can stimulate the GDP-GTP exchange of the isoprenylated form of Cdc42Hs. It also stimulates the mitogen activated protein kinase cascade leading to c-Jun kinase SAPK/JNK1 activation. Defects in this gene are the cause of the faciogenital dysplasia in Aarskog-Scott syndrome and a syndromatic form of X-linked cognitive disability. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant X-54455400-C-G is Benign according to our data. Variant chrX-54455400-C-G is described in ClinVar as [Benign]. Clinvar id is 259403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGD1 | NM_004463.3 | c.2015+48G>C | intron_variant | ENST00000375135.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGD1 | ENST00000375135.4 | c.2015+48G>C | intron_variant | 1 | NM_004463.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.366 AC: 40741AN: 111400Hom.: 9188 Cov.: 23 AF XY: 0.354 AC XY: 11885AN XY: 33588
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GnomAD3 exomes AF: 0.269 AC: 43883AN: 163058Hom.: 7195 AF XY: 0.242 AC XY: 12522AN XY: 51698
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GnomAD4 exome AF: 0.185 AC: 168877AN: 912129Hom.: 18293 Cov.: 16 AF XY: 0.192 AC XY: 49806AN XY: 259181
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GnomAD4 genome AF: 0.366 AC: 40792AN: 111455Hom.: 9193 Cov.: 23 AF XY: 0.355 AC XY: 11931AN XY: 33651
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at