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GeneBe

X-138632895-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_004114.5(FGF13):c.693C>T(p.Gly231=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00074 in 1,208,102 control chromosomes in the GnomAD database, including 2 homozygotes. There are 349 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00062 ( 0 hom., 21 hem., cov: 22)
Exomes 𝑓: 0.00075 ( 2 hom. 328 hem. )

Consequence

FGF13
NM_004114.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.679
Variant links:
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-138632895-G-A is Benign according to our data. Variant chrX-138632895-G-A is described in ClinVar as [Benign]. Clinvar id is 710910.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.679 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000752 (825/1097170) while in subpopulation MID AF= 0.00729 (30/4115). AF 95% confidence interval is 0.00525. There are 2 homozygotes in gnomad4_exome. There are 328 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 21 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGF13NM_004114.5 linkuse as main transcriptc.693C>T p.Gly231= synonymous_variant 5/5 ENST00000315930.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGF13ENST00000315930.11 linkuse as main transcriptc.693C>T p.Gly231= synonymous_variant 5/51 NM_004114.5 P4Q92913-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000622
AC:
69
AN:
110877
Hom.:
0
Cov.:
22
AF XY:
0.000634
AC XY:
21
AN XY:
33115
show subpopulations
Gnomad AFR
AF:
0.0000986
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000578
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00348
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00422
Gnomad NFE
AF:
0.000944
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000819
AC:
150
AN:
183159
Hom.:
0
AF XY:
0.00114
AC XY:
77
AN XY:
67599
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000220
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00258
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00108
Gnomad OTH exome
AF:
0.00155
GnomAD4 exome
AF:
0.000752
AC:
825
AN:
1097170
Hom.:
2
Cov.:
30
AF XY:
0.000905
AC XY:
328
AN XY:
362580
show subpopulations
Gnomad4 AFR exome
AF:
0.000227
Gnomad4 AMR exome
AF:
0.000369
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00246
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000708
Gnomad4 OTH exome
AF:
0.00102
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000622
AC:
69
AN:
110932
Hom.:
0
Cov.:
22
AF XY:
0.000633
AC XY:
21
AN XY:
33180
show subpopulations
Gnomad4 AFR
AF:
0.0000984
Gnomad4 AMR
AF:
0.000577
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00349
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000944
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000825
Hom.:
5
Bravo
AF:
0.000506

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeOct 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
Cadd
Benign
2.3
Dann
Benign
0.57
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs374129615; hg19: chrX-137715056; COSMIC: COSV59544261; COSMIC: COSV59544261; API