13-102177067-C-T

Variant summary

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

The ENST00000376131.9(FGF14):c.208+224404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0504 in 152,200 control chromosomes in the GnomAD database, including 234 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 0.050 (234 hom., cov: 33)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF14	NM_001321931.1	c.-60+16056G>A		intron_variant
FGF14	NM_001321932.1	c.4+15970G>A		intron_variant
FGF14	NM_001321933.1	c.13+43630G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF14	ENST00000376131.9	c.208+224404G>A		intron_variant		1
FGF14	ENST00000418923.3	c.91+224404G>A		intron_variant		3		A1
FGF14	ENST00000706494.1	c.-60+189378G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0505 AC: 7675 AN: 152082 Hom.: 237 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0504 AC: 7673 AN: 152200 Hom.: 234 Cov.: 33 AF XY: 0.0506 AC XY: 3761 AN XY: 74392

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0555

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0699

Gnomad4 FIN AF: 0.0599

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0609 Hom.: 431

Bravo AF: 0.0478

Asia WGS AF: 0.0400 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7995765; hg19: chr13-102829417;