rs4073716

Variant names:

• chr5-171437235-A-G
• rs4073716
• NM_003862.3:c.250+962A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-171437235-A-G
• chr5-171437235-A-T

Variant summary

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

The NM_003862.3(FGF18):​c.250+962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,056 control chromosomes in the GnomAD database, including 21,923 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 0.53 (21923 hom., cov: 33)
• Consequence: FGF18 NM_003862.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF18	NM_003862.3	c.250+962A>G		intron_variant	Intron 3 of 4	ENST00000274625.6	NP_003853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF18	ENST00000274625.6	c.250+962A>G		intron_variant	Intron 3 of 4	1	NM_003862.3	ENSP00000274625.5

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81211 AN: 151938 Hom.: 21881 Cov.: 33

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.535 AC: 81301 AN: 152056 Hom.: 21923 Cov.: 33 AF XY: 0.532 AC XY: 39531 AN XY: 74314

African (AFR) AF: 0.601 AC: 24921 AN: 41488

American (AMR) AF: 0.485 AC: 7412 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2816 AN: 5134

South Asian (SAS) AF: 0.585 AC: 2821 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5051 AN: 10592

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34519 AN: 67940

Other (OTH) AF: 0.538 AC: 1136 AN: 2112

Alfa AF: 0.519 Hom.: 10356

Bravo AF: 0.534

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.76
PhyloP100		1.8
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: rs4073716; hg19: chr5-170864239;