rs17407577

chr4-122858186-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001361665.2(FGF2):c.179-18135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 152,242 control chromosomes in the GnomAD database, including 168 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 0.044 (168 hom., cov: 32)
• Consequence: FGF2 NM_001361665.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

FGF2 (HGNC:3676): (fibroblast growth factor 2) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members bind heparin and possess broad mitogenic and angiogenic activities. This protein has been implicated in diverse biological processes, such as limb and nervous system development, wound healing, and tumor growth. The mRNA for this gene contains multiple polyadenylation sites, and is alternatively translated from non-AUG (CUG) and AUG initiation codons, resulting in five different isoforms with distinct properties. The CUG-initiated isoforms are localized in the nucleus and are responsible for the intracrine effect, whereas, the AUG-initiated form is mostly cytosolic and is responsible for the paracrine and autocrine effects of this FGF. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF2	NM_001361665.2	c.179-18135T>C		intron_variant		ENST00000644866.2
FGF2	NM_002006.6	c.578-18135T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF2	ENST00000644866.2	c.179-18135T>C		intron_variant			NM_001361665.2	P1
FGF2	ENST00000264498.9	c.578-18135T>C		intron_variant		1
FGF2	ENST00000608478.1	c.179-18135T>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6762 AN: 152124 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0444 AC: 6765 AN: 152242 Hom.: 168 Cov.: 32 AF XY: 0.0418 AC XY: 3110 AN XY: 74440

Gnomad4 AFR AF: 0.0388

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0586

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0545 Hom.: 325

Bravo AF: 0.0455

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	12
Dann	Benign	0.91

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

Other links and lift over

dbSNP: rs17407577; hg19: chr4-123779341;