Genetic Variant FGF21:c.*206G>T (chr19-48758426-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019113.4(FGF21):c.*206G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0965 in 454,270 control chromosomes in the GnomAD database, including 5,483 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 0.13 ( 2630 hom., cov: 31)

Exomes 𝑓: 0.079 ( 2853 hom. )

Consequence

FGF21
NM_019113.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Variant links:

Genes affected

FGF21 (HGNC:3678): (fibroblast growth factor 21) Theis gene encodes 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. This protein is a secreted endocrine factor that functions as a major metabolic regulator. The encoded protein stimulates the uptake of glucose in adipose tissue. [provided by RefSeq, Mar 2016]

FGF21 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF21	NM_019113.4 link	c.*206G>T		downstream_gene_variant		ENST00000593756.6	NP_061986.1	Q9NSA1A0A7U3L5M7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF21	ENST00000593756.6 link	c.*206G>T		downstream_gene_variant		1	NM_019113.4	ENSP00000471477.1		Q9NSA1
FGF21	ENST00000222157.5 link	c.*206G>T		downstream_gene_variant		1		ENSP00000222157.3		Q9NSA1

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

19998

AN:

151558

Hom.:

2609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.0272

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0277

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0343

Gnomad OTH

AF:

0.0993

GnomAD4 exome

AF:

0.0785

AC:

23760

AN:

302602

Hom.:

2853

AF XY:

0.0763

AC XY:

11879

AN XY:

155634

show subpopulations

Gnomad4 AFR exome

AF:

0.327

Gnomad4 AMR exome

AF:

0.119

Gnomad4 ASJ exome

AF:

0.0222

Gnomad4 EAS exome

AF:

0.407

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0245

Gnomad4 NFE exome

AF:

0.0349

Gnomad4 OTH exome

AF:

0.0788

GnomAD4 genome

AF:

0.132

AC:

20058

AN:

151668

Hom.:

2630

Cov.:

AF XY:

0.133

AC XY:

9850

AN XY:

74126

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.111

Gnomad4 ASJ

AF:

0.0272

Gnomad4 EAS

AF:

0.274

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.0277

Gnomad4 NFE

AF:

0.0343

Gnomad4 OTH

AF:

0.0992

Alfa

AF:

0.0171

Hom.:

Bravo

AF:

0.149

Asia WGS

AF:

0.222

AC:

770

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.13

DANN

Benign

0.54

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over