rs7337292

Positions:

• chr13-102046065-A-G

Variant summary

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

The ENST00000376131.9(FGF14):​c.209-170769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 154,140 control chromosomes in the GnomAD database, including 17,898 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 0.47 (17616 hom., cov: 32)
  • Exomes 𝑓: 0.51 (282 hom.)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF14	NM_001321931.1	c.-60+147058T>C		intron_variant			NP_001308860.1
FGF14	NM_001321932.1	c.4+146972T>C		intron_variant			NP_001308861.1
FGF14	NM_001321933.1	c.14-170769T>C		intron_variant			NP_001308862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.209-170769T>C		intron_variant		1		ENSP00000365301
FGF14	ENST00000418923.3	c.92-170769T>C		intron_variant		3		ENSP00000516414	A1
FGF14	ENST00000706494.1	c.-59-170769T>C		intron_variant				ENSP00000516417

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71703 AN: 151842 Hom.: 17595 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.489

GnomAD4 exome AF: 0.507 AC: 1105 AN: 2178 Hom.: 282 AF XY: 0.494 AC XY: 535 AN XY: 1084

Gnomad4 AFR exome AF: 0.568

Gnomad4 AMR exome AF: 0.875

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.383

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.473

GnomAD4 genome AF: 0.472 AC: 71767 AN: 151962 Hom.: 17616 Cov.: 32 AF XY: 0.471 AC XY: 34980 AN XY: 74258

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.487

Alfa AF: 0.452 Hom.: 2722

Bravo AF: 0.492

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7337292; hg19: chr13-102698415;