rs4772445

Variant names:

• chr13-102151281-G-A
• rs4772445
• ENST00000376131.9:c.208+250190C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-102151281-G-A
• chr13-102151281-G-C

Variant summary

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

The NM_175929.3(FGF14):​c.208+250190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,026 control chromosomes in the GnomAD database, including 2,817 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 0.19 (2817 hom., cov: 32)
• Consequence: FGF14 NM_175929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF14	NM_175929.3	c.208+250190C>T		intron_variant	Intron 1 of 4		NP_787125.1
FGF14	NM_001321939.2	c.208+250190C>T		intron_variant	Intron 1 of 3		NP_001308868.1
FGF14	NM_001321945.2	c.91+250190C>T		intron_variant	Intron 2 of 5		NP_001308874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.208+250190C>T		intron_variant	Intron 1 of 4	1		ENSP00000365301.3
FGF14	ENST00000418923.3	c.91+250190C>T		intron_variant	Intron 2 of 5	3		ENSP00000516414.1
FGF14	ENST00000706494.1	c.-60+215164C>T		intron_variant	Intron 3 of 6			ENSP00000516417.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28572 AN: 151908 Hom.: 2815 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28604 AN: 152026 Hom.: 2817 Cov.: 32 AF XY: 0.194 AC XY: 14427 AN XY: 74304

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.184

Alfa AF: 0.162 Hom.: 4029

Bravo AF: 0.187

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
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: rs4772445; hg19: chr13-102803631;