X-138649185-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004114.5(FGF13):c.403-13530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.68 (19023 hom., 22033 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: FGF13 NM_004114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 19018 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF13	NM_004114.5	c.403-13530A>G		intron_variant		ENST00000315930.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF13	ENST00000315930.11	c.403-13530A>G		intron_variant		1	NM_004114.5	P4

Frequencies

GnomAD3 genomes AF: 0.677 AC: 74770 AN: 110466 Hom.: 19018 Cov.: 23 AF XY: 0.672 AC XY: 21975 AN XY: 32688

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.654

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.677 AC: 74832 AN: 110518 Hom.: 19023 Cov.: 23 AF XY: 0.673 AC XY: 22033 AN XY: 32750

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.655

Alfa AF: 0.612 Hom.: 10237

Bravo AF: 0.694

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.86
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs2267628; hg19: chrX-137731346;