rs1542409

Positions:

• chr13-102046711-A-G
• chr13-102046711-A-T

Variant summary

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

The ENST00000376131.9(FGF14):​c.209-171415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,084 control chromosomes in the GnomAD database, including 17,654 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 (17654 hom., cov: 33)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

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=-0.87).
• 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+146412T>C		intron_variant			NP_001308860.1
FGF14	NM_001321932.1	c.4+146326T>C		intron_variant			NP_001308861.1
FGF14	NM_001321933.1	c.14-171415T>C		intron_variant			NP_001308862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.209-171415T>C		intron_variant		1		ENSP00000365301
FGF14	ENST00000418923.3	c.92-171415T>C		intron_variant		3		ENSP00000516414	A1
FGF14	ENST00000706494.1	c.-59-171415T>C		intron_variant				ENSP00000516417

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71775 AN: 151966 Hom.: 17634 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.726

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

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

GnomAD4 genome AF: 0.472 AC: 71838 AN: 152084 Hom.: 17654 Cov.: 33 AF XY: 0.471 AC XY: 35027 AN XY: 74334

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.487

Alfa AF: 0.423 Hom.: 7400

Bravo AF: 0.492

Asia WGS AF: 0.548 AC: 1903 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1542409; hg19: chr13-102699061;