13-102060909-C-T

Position:

• chr13-102060909-C-T

Variant summary

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

The ENST00000376131.9(FGF14):​c.209-185613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,992 control chromosomes in the GnomAD database, including 11,921 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 0.39 (11921 hom., cov: 32)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF14	NM_001321931.1	c.-60+132214G>A		intron_variant
FGF14	NM_001321932.1	c.4+132128G>A		intron_variant
FGF14	NM_001321933.1	c.13+159788G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF14	ENST00000376131.9	c.209-185613G>A		intron_variant		1
FGF14	ENST00000418923.3	c.92-185613G>A		intron_variant		3		A1
FGF14	ENST00000706494.1	c.-59-185613G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58771 AN: 151874 Hom.: 11911 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.387 AC: 58822 AN: 151992 Hom.: 11921 Cov.: 32 AF XY: 0.389 AC XY: 28931 AN XY: 74284

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.390

Alfa AF: 0.382 Hom.: 2105

Bravo AF: 0.397

Asia WGS AF: 0.526 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7992504; hg19: chr13-102713259;