NM_003862.3:c.358-936A>G

Variant names:

• chr5-171455603-A-G
• rs2043278
• NM_003862.3:c.358-936A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003862.3(FGF18):​c.358-936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,148 control chromosomes in the GnomAD database, including 47,346 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 0.78 (47346 hom., cov: 32)
• Consequence: FGF18 NM_003862.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 6 publications found

Genes affected

FGF18 (HGNC:3674): (fibroblast growth factor 18) The protein encoded by this gene is 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, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth, and invasion. It has been shown in vitro that this protein is able to induce neurite outgrowth in PC12 cells. Studies of the similar proteins in mouse and chick suggested that this protein is a pleiotropic growth factor that stimulates proliferation in a number of tissues, most notably the liver and small intestine. Knockout studies of the similar gene in mice implied the role of this protein in regulating proliferation and differentiation of midline cerebellar structures. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF18	NM_003862.3	c.358-936A>G		intron_variant	Intron 4 of 4	ENST00000274625.6	NP_003853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF18	ENST00000274625.6	c.358-936A>G		intron_variant	Intron 4 of 4	1	NM_003862.3	ENSP00000274625.5

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119249 AN: 152030 Hom.: 47304 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.776

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.784 AC: 119350 AN: 152148 Hom.: 47346 Cov.: 32 AF XY: 0.782 AC XY: 58146 AN XY: 74368

African (AFR) AF: 0.889 AC: 36932 AN: 41532

American (AMR) AF: 0.821 AC: 12554 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2601 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2802 AN: 5152

South Asian (SAS) AF: 0.699 AC: 3365 AN: 4812

European-Finnish (FIN) AF: 0.727 AC: 7694 AN: 10578

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50933 AN: 67992

Other (OTH) AF: 0.777 AC: 1640 AN: 2110

Alfa AF: 0.761 Hom.: 189268

Bravo AF: 0.799

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.68
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2043278; hg19: chr5-170882607;