rs1336708

chr13-102312653-A-G

Variant summary

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

The ENST00000376131.9(FGF14):c.208+88818T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,070 control chromosomes in the GnomAD database, including 6,322 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 0.27 (6322 hom., cov: 32)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367

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]

FGF14-IT1 (HGNC:42774): (FGF14 intronic transcript 1)

LOC107984615 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF14-IT1	NR_036486.1	n.410-18613T>C		intron_variant, non_coding_transcript_variant
LOC107984615	XR_007063856.1	n.353-90A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF14-IT1	ENST00000607251.5	n.410-18613T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41782 AN: 151952 Hom.: 6318 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.275 AC: 41810 AN: 152070 Hom.: 6322 Cov.: 32 AF XY: 0.269 AC XY: 19970 AN XY: 74340

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.285

Alfa AF: 0.249 Hom.: 2352

Bravo AF: 0.282

Asia WGS AF: 0.213 AC: 742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336708; hg19: chr13-102965003;