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 NM_005130.5(FGFBP1):c.*466G>A variant causes a downstream gene 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
NM_005130.5 downstream_gene

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:

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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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFBP1	NM_005130.5 link	c.*466G>A		downstream_gene_variant		ENST00000382333.2	NP_005121.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFBP1	ENST00000382333.2 link	c.*466G>A		downstream_gene_variant		3	NM_005130.5	ENSP00000371770.1

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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over