rs17515365

Positions:

• chr8-16992247-T-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_019851.3(FGF20):​c.*824_*825insT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.179 in 152,080 control chromosomes in the GnomAD database, including 2,888 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (2888 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: FGF20 NM_019851.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.91

Genes affected

FGF20 (HGNC:3677): (fibroblast growth factor 20) The protein encoded by this gene is a member of the fibroblast growth factor family. The fibroblast growth factors 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. This gene product is a secreted neurotrophic factor but lacks a typical signal peptide. It is expressed in normal brain, particularly the cerebellum, and may regulate central nervous system development and function. Homodimerization of this protein was shown to regulate its receptor binding activity and concentration gradient in the extracellular matrix. Genetic variations of this gene have been associated with Parkinson disease susceptibility. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF20	NM_019851.3	c.*824_*825insT		3_prime_UTR_variant	3/3	ENST00000180166.6	NP_062825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF20	ENST00000180166.6	c.*824_*825insT		3_prime_UTR_variant	3/3	1	NM_019851.3	ENSP00000180166	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27179 AN: 151962 Hom.: 2871 Cov.: 28

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.182

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.179 AC: 27231 AN: 152080 Hom.: 2888 Cov.: 28 AF XY: 0.180 AC XY: 13418 AN XY: 74358

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.187

Alfa AF: 0.150 Hom.: 223

Bravo AF: 0.192

Asia WGS AF: 0.329 AC: 1138 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17515365; hg19: chr8-16849756;