Genetic Variant FGFR4:p.Arg234Arg (chr5-177091783-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_213647.3(FGFR4):c.702C>T(p.Arg234Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 1,613,994 control chromosomes in the GnomAD database, including 481,490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.75 ( 42857 hom., cov: 33)

Exomes 𝑓: 0.77 ( 438633 hom. )

Consequence

FGFR4
NM_213647.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.204

Variant links:

Genes affected

FGFR4 (HGNC:3691): (fibroblast growth factor receptor 4) The protein encoded by this gene is a tyrosine kinase and cell surface receptor for fibroblast growth factors. The encoded protein is involved in the regulation of several pathways, including cell proliferation, cell differentiation, cell migration, lipid metabolism, bile acid biosynthesis, vitamin D metabolism, glucose uptake, and phosphate homeostasis. This protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment, and a cytoplasmic tyrosine kinase domain. The extracellular portion interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. [provided by RefSeq, Aug 2017]

FGFR4 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=-0.62).

BP6

Variant 5-177091783-C-T is Benign according to our data. Variant chr5-177091783-C-T is described in ClinVar as [Benign]. Clinvar id is 3060679.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.204 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR4	NM_213647.3 link	c.702C>T	p.Arg234Arg	synonymous_variant	Exon 6 of 18	ENST00000292408.9	NP_998812.1	P22455-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR4	ENST00000292408.9 link	c.702C>T	p.Arg234Arg	synonymous_variant	Exon 6 of 18	1	NM_213647.3	ENSP00000292408.4		P22455-1

Frequencies

GnomAD3 genomes

AF:

0.746

AC:

113479

AN:

152056

Hom.:

42798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.661

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.788

Gnomad ASJ

AF:

0.766

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.893

Gnomad FIN

AF:

0.818

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.748

Gnomad OTH

AF:

0.742

GnomAD3 exomes

AF:

0.801

AC:

201253

AN:

251390

Hom.:

81543

AF XY:

0.802

AC XY:

108941

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.652

Gnomad AMR exome

AF:

0.863

Gnomad ASJ exome

AF:

0.755

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.885

Gnomad FIN exome

AF:

0.813

Gnomad NFE exome

AF:

0.751

Gnomad OTH exome

AF:

0.778

GnomAD4 exome

AF:

0.772

AC:

1128966

AN:

1461820

Hom.:

438633

Cov.:

AF XY:

0.774

AC XY:

563147

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.661

Gnomad4 AMR exome

AF:

0.856

Gnomad4 ASJ exome

AF:

0.755

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.879

Gnomad4 FIN exome

AF:

0.811

Gnomad4 NFE exome

AF:

0.755

Gnomad4 OTH exome

AF:

0.776

GnomAD4 genome

AF:

0.747

AC:

113599

AN:

152174

Hom.:

42857

Cov.:

AF XY:

0.753

AC XY:

56027

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.661

Gnomad4 AMR

AF:

0.788

Gnomad4 ASJ

AF:

0.766

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.894

Gnomad4 FIN

AF:

0.818

Gnomad4 NFE

AF:

0.748

Gnomad4 OTH

AF:

0.746

Alfa

AF:

0.747

Hom.:

27651

Bravo

AF:

0.739

Asia WGS

AF:

0.926

AC:

3222

AN:

3478

EpiCase

AF:

0.733

EpiControl

AF:

0.740

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FGFR4-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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