13-102048769-C-T

Position:

• chr13-102048769-C-T

Variant summary

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

The NM_175929.3(FGF14):​c.209-173473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,960 control chromosomes in the GnomAD database, including 10,855 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 0.37 (10855 hom., cov: 32)
• Consequence: FGF14 NM_175929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF14	NM_175929.3	c.209-173473G>A		intron_variant			NP_787125.1
FGF14	NM_001321939.2	c.209-179941G>A		intron_variant			NP_001308868.1
FGF14	NM_001321945.2	c.92-173473G>A		intron_variant			NP_001308874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.209-173473G>A		intron_variant		1		ENSP00000365301.3
FGF14	ENST00000418923.3	c.92-173473G>A		intron_variant		3		ENSP00000516414.1
FGF14	ENST00000706494.1	c.-59-173473G>A		intron_variant				ENSP00000516417.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55486 AN: 151842 Hom.: 10853 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.365 AC: 55500 AN: 151960 Hom.: 10855 Cov.: 32 AF XY: 0.369 AC XY: 27427 AN XY: 74284

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.395

Alfa AF: 0.373 Hom.: 17337

Bravo AF: 0.373

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.064
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457315; hg19: chr13-102701119; COSMIC: COSV65938248; COSMIC: COSV65938248;