Genetic Variant NM_019851.3:c.*182C>T (chr8-16992890-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_019851.3(FGF20):c.*182C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 666,364 control chromosomes in the GnomAD database, including 1,821 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 294 hom., cov: 32)

Exomes 𝑓: 0.070 ( 1527 hom. )

Consequence

FGF20
NM_019851.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts U:1B:2

Conservation

PhyloP100: 0.460

Variant links:

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]

FGF20 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 8-16992890-G-A is Benign according to our data. Variant chr8-16992890-G-A is described in ClinVar as [Benign]. Clinvar id is 4885.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.083 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF20	NM_019851.3 link	c.*182C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000180166.6	NP_062825.1	Q9NP95A0A7U3L649

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF20	ENST00000180166 link	c.*182C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_019851.3	ENSP00000180166.5		Q9NP95
FGF20	ENST00000519941.1 link	c.*182C>T		downstream_gene_variant		5		ENSP00000428072.1		H0YAT9

Frequencies

GnomAD3 genomes

AF:

0.0545

AC:

8291

AN:

152024

Hom.:

294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0531

Gnomad ASJ

AF:

0.0380

Gnomad EAS

AF:

0.00675

Gnomad SAS

AF:

0.0491

Gnomad FIN

AF:

0.0350

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.0848

Gnomad OTH

AF:

0.0636

GnomAD4 exome

AF:

0.0703

AC:

36164

AN:

514222

Hom.:

1527

Cov.:

AF XY:

0.0696

AC XY:

18764

AN XY:

269530

show subpopulations

Gnomad4 AFR exome

AF:

0.0149

Gnomad4 AMR exome

AF:

0.0452

Gnomad4 ASJ exome

AF:

0.0337

Gnomad4 EAS exome

AF:

0.00395

Gnomad4 SAS exome

AF:

0.0484

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.0880

Gnomad4 OTH exome

AF:

0.0621

GnomAD4 genome

AF:

0.0545

AC:

8288

AN:

152142

Hom.:

294

Cov.:

AF XY:

0.0517

AC XY:

3847

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.0169

Gnomad4 AMR

AF:

0.0531

Gnomad4 ASJ

AF:

0.0380

Gnomad4 EAS

AF:

0.00658

Gnomad4 SAS

AF:

0.0494

Gnomad4 FIN

AF:

0.0350

Gnomad4 NFE

AF:

0.0848

Gnomad4 OTH

AF:

0.0630

Alfa

AF:

0.0757

Hom.:

308

Bravo

AF:

0.0534

Asia WGS

AF:

0.0310

AC:

107

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 20427658, 18252210, 30241547) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Parkinson disease, late-onset

Uncertain:1

Feb 15, 2009

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.2

DANN

Benign

0.48

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over