Variant 8-16993428-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_019851.3(FGF20):c.391-111C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 1,124,344 control chromosomes in the GnomAD database, including 3,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.062 ( 465 hom., cov: 32)

Exomes 𝑓: 0.076 ( 3302 hom. )

Consequence

FGF20
NM_019851.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.110

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 8-16993428-G-T is Benign according to our data. Variant chr8-16993428-G-T is described in ClinVar as [Benign]. Clinvar id is 1284084.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF20	NM_019851.3 linkuse as main transcript	c.391-111C>A		intron_variant		ENST00000180166.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF20	ENST00000180166.6 linkuse as main transcript	c.391-111C>A		intron_variant		1	NM_019851.3	P1
FGF20	ENST00000519941.1 linkuse as main transcript	c.95-111C>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0617

AC:

9372

AN:

151844

Hom.:

465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0159

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0428

Gnomad ASJ

AF:

0.0364

Gnomad EAS

AF:

0.00232

Gnomad SAS

AF:

0.0564

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0824

Gnomad OTH

AF:

0.0489

GnomAD4 exome

AF:

0.0757

AC:

73619

AN:

972388

Hom.:

3302

AF XY:

0.0750

AC XY:

36835

AN XY:

490922

show subpopulations

Gnomad4 AFR exome

AF:

0.0134

Gnomad4 AMR exome

AF:

0.0284

Gnomad4 ASJ exome

AF:

0.0371

Gnomad4 EAS exome

AF:

0.000678

Gnomad4 SAS exome

AF:

0.0590

Gnomad4 FIN exome

AF:

0.159

Gnomad4 NFE exome

AF:

0.0818

Gnomad4 OTH exome

AF:

0.0676

GnomAD4 genome

AF:

0.0616

AC:

9367

AN:

151956

Hom.:

465

Cov.:

AF XY:

0.0651

AC XY:

4835

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.0159

Gnomad4 AMR

AF:

0.0427

Gnomad4 ASJ

AF:

0.0364

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.0562

Gnomad4 FIN

AF:

0.180

Gnomad4 NFE

AF:

0.0823

Gnomad4 OTH

AF:

0.0488

Alfa

AF:

0.0275

Hom.:

Bravo

AF:

0.0480

Asia WGS

AF:

0.0450

AC:

154

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.1

DANN

Benign

0.66

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