4-15938292-C-G

Position:

• chr4-15938292-C-G

Variant summary

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

The NM_005130.5(FGFBP1):​c.-62G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,258 control chromosomes in the GnomAD database, including 52,717 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 0.83 (52690 hom., cov: 32)
  • Exomes 𝑓: 0.79 (27 hom.)
• Consequence: FGFBP1 NM_005130.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

FGFBP1 (HGNC:19695): (fibroblast growth factor binding protein 1) This gene encodes a secreted fibroblast growth factor carrier protein. The encoded protein plays a critical role in cell proliferation, differentiation and migration by binding to fibroblast growth factors and potentiating their biological effects on target cells. The encoded protein may also play a role in tumor growth as an angiogenic switch molecule, and expression of this gene has been associated with several types of cancer including pancreatic and colorectal adenocarcinoma. A pseudogene of this gene is also located on the short arm of chromosome 4. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGFBP1	NM_005130.5	c.-62G>C		5_prime_UTR_variant	2/3	ENST00000382333.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGFBP1	ENST00000382333.2	c.-62G>C		5_prime_UTR_variant	2/3	3	NM_005130.5	P1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126092 AN: 152050 Hom.: 52664 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.833

GnomAD4 exome AF: 0.789 AC: 71 AN: 90 Hom.: 27 Cov.: 0 AF XY: 0.778 AC XY: 56 AN XY: 72

Gnomad4 AFR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.788

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.829 AC: 126165 AN: 152168 Hom.: 52690 Cov.: 32 AF XY: 0.829 AC XY: 61675 AN XY: 74394

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.831

Alfa AF: 0.856 Hom.: 6548

Bravo AF: 0.818

Asia WGS AF: 0.680 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.080
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2245964; hg19: chr4-15939915;