rs6491679

Positions:

• chr13-102278224-T-G

Variant summary

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

The NM_175929.3(FGF14):​c.208+123247A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,032 control chromosomes in the GnomAD database, including 7,287 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 0.30 (7287 hom., cov: 32)
• Consequence: FGF14 NM_175929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF14	NM_175929.3	c.208+123247A>C		intron_variant			NP_787125.1
FGF14	NM_001321939.2	c.208+123247A>C		intron_variant			NP_001308868.1
FGF14	NM_001321945.2	c.91+123247A>C		intron_variant			NP_001308874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.208+123247A>C		intron_variant		1		ENSP00000365301.3
FGF14	ENST00000418923.3	c.91+123247A>C		intron_variant		3		ENSP00000516414.1
FGF14	ENST00000706494.1	c.-60+88221A>C		intron_variant				ENSP00000516417.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45801 AN: 151914 Hom.: 7287 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.301 AC: 45823 AN: 152032 Hom.: 7287 Cov.: 32 AF XY: 0.295 AC XY: 21898 AN XY: 74316

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.317

Alfa AF: 0.265 Hom.: 3002

Bravo AF: 0.304

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.95
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6491679; hg19: chr13-102930574;