Genetic Variant FGFBP1:c.*466G>A (chr4-15935462-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000888688.1(FGFBP1):c.*466G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,888 control chromosomes in the GnomAD database, including 13,945 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 0.41 ( 13877 hom., cov: 33)

Exomes 𝑓: 0.40 ( 68 hom. )

Consequence

FGFBP1
ENST00000888688.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

Publications

2 publications found

Variant links:

COSMIC-nc: COSV52586255

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]

FGFBP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000888688.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGFBP1	NM_005130.5	MANE Select	c.*466G>A		downstream_gene	N/A	NP_005121.1	Q14512

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGFBP1	ENST00000888688.1		c.*466G>A	3_prime_UTR	Exon 3 of 3	ENSP00000558747.1
FGFBP1	ENST00000382333.2	TSL:3 MANE Select	c.*466G>A	downstream_gene	N/A	ENSP00000371770.1	Q14512
FGFBP1	ENST00000888689.1		c.*466G>A	downstream_gene	N/A	ENSP00000558748.1

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62573

AN:

151956

Hom.:

13866

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.442

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.421

GnomAD4 exome

AF:

0.402

AC:

327

AN:

814

Hom.:

AF XY:

0.366

AC XY:

145

AN XY:

396

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.550

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.398

AC:

245

AN:

616

Other (OTH)

AF:

0.447

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.412

AC:

62600

AN:

152074

Hom.:

13877

Cov.:

AF XY:

0.417

AC XY:

30978

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.262

AC:

10854

AN:

41472

American (AMR)

AF:

0.441

AC:

6738

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

1389

AN:

3472

East Asian (EAS)

AF:

0.581

AC:

3009

AN:

5178

South Asian (SAS)

AF:

0.269

AC:

1295

AN:

4814

European-Finnish (FIN)

AF:

0.590

AC:

6239

AN:

10578

Middle Eastern (MID)

AF:

0.442

AC:

129

AN:

292

European-Non Finnish (NFE)

AF:

0.468

AC:

31780

AN:

67972

Other (OTH)

AF:

0.416

AC:

878

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1832

3664

5497

7329

9161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.420

Hom.:

5417

Bravo

AF:

0.398

Asia WGS

AF:

0.376

AC:

1308

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

(source)

DANN

Benign

0.92

PhyloP100

0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over