rs9518638

Variant names:

• chr13-102124375-G-T
• rs9518638
• ENST00000376131.9:c.209-249079C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175929.3(FGF14):​c.209-249079C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,932 control chromosomes in the GnomAD database, including 3,259 homozygotes. 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 0.20 (3259 hom., cov: 32)
• Consequence: FGF14 NM_175929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

FGF14 (HGNC:3671): (fibroblast growth factor 14) 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. A mutation in this gene is associated with autosomal dominant cerebral ataxia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF14	NM_175929.3	c.209-249079C>A		intron_variant	Intron 1 of 4		NP_787125.1
FGF14	NM_001321939.2	c.209-255547C>A		intron_variant	Intron 1 of 3		NP_001308868.1
FGF14	NM_001321945.2	c.92-249079C>A		intron_variant	Intron 2 of 5		NP_001308874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.209-249079C>A		intron_variant	Intron 1 of 4	1		ENSP00000365301.3
FGF14	ENST00000418923.3	c.92-249079C>A		intron_variant	Intron 2 of 5	3		ENSP00000516414.1
FGF14	ENST00000706494.1	c.-60+242070C>A		intron_variant	Intron 3 of 6			ENSP00000516417.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30507 AN: 151814 Hom.: 3256 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.201 AC: 30530 AN: 151932 Hom.: 3259 Cov.: 32 AF XY: 0.200 AC XY: 14848 AN XY: 74262

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0660

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.227

Alfa AF: 0.213 Hom.: 571

Bravo AF: 0.208

Asia WGS AF: 0.130 AC: 451 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9518638; hg19: chr13-102776725;