chrX-138710845-G-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_004114.5(FGF13):c.159C>A(p.Gly53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,211,016 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000097 ( 0 hom., 3 hem., cov: 25)
Exomes 𝑓: 0.000012 ( 0 hom. 2 hem. )
Consequence
FGF13
NM_004114.5 synonymous
NM_004114.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.15
Genes affected
FGF13 (HGNC:3670): (fibroblast growth factor 13) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth, and invasion. This gene is located in a region on chromosome X, which is associated with Borjeson-Forssman-Lehmann syndrome (BFLS), making it a possible candidate gene for familial cases of the BFLS, and for other syndromal and nonspecific forms of X-linked cognitive disability mapping to this region. Alternative splicing of this gene at the 5' end results in several transcript variants encoding different isoforms with different N-termini. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
Variant X-138710845-G-T is Benign according to our data. Variant chrX-138710845-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 758760.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.14 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF13 | NM_004114.5 | c.159C>A | p.Gly53= | synonymous_variant | 1/5 | ENST00000315930.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF13 | ENST00000315930.11 | c.159C>A | p.Gly53= | synonymous_variant | 1/5 | 1 | NM_004114.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000974 AC: 11AN: 112927Hom.: 0 Cov.: 25 AF XY: 0.0000855 AC XY: 3AN XY: 35071
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GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183090Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67572
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GnomAD4 exome AF: 0.0000118 AC: 13AN: 1098089Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 2AN XY: 363447
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GnomAD4 genome AF: 0.0000974 AC: 11AN: 112927Hom.: 0 Cov.: 25 AF XY: 0.0000855 AC XY: 3AN XY: 35071
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at