13-102048494-C-T

Position:

• chr13-102048494-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.209-173198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,960 control chromosomes in the GnomAD database, including 25,586 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 0.54 (25586 hom., cov: 32)
• Consequence: FGF14 NM_175929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF14	NM_175929.3	c.209-173198G>A		intron_variant			NP_787125.1
FGF14	NM_001321939.2	c.209-179666G>A		intron_variant			NP_001308868.1
FGF14	NM_001321945.2	c.92-173198G>A		intron_variant			NP_001308874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.209-173198G>A		intron_variant		1		ENSP00000365301.3
FGF14	ENST00000418923.3	c.92-173198G>A		intron_variant		3		ENSP00000516414.1
FGF14	ENST00000706494.1	c.-59-173198G>A		intron_variant				ENSP00000516417.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82354 AN: 151842 Hom.: 25544 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.543 AC: 82445 AN: 151960 Hom.: 25586 Cov.: 32 AF XY: 0.540 AC XY: 40074 AN XY: 74268

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.539

Alfa AF: 0.467 Hom.: 2314

Bravo AF: 0.574

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs636674; hg19: chr13-102700844;