dbSNP rs2531174: FGFBP1:c.-242+105C>T (chr4-15938582-G-A) – 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.-242+105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,468 control chromosomes in the GnomAD database, including 68,911 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 0.95 ( 68801 hom., cov: 31)

Exomes 𝑓: 0.97 ( 110 hom. )

Consequence

FGFBP1
NM_005130.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Publications

1 publications found

Variant links:

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005130.5. 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.-242+105C>T		intron	N/A	NP_005121.1	Q14512

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGFBP1	ENST00000382333.2	TSL:3 MANE Select	c.-242+105C>T	intron	N/A	ENSP00000371770.1	Q14512
FGFBP1	ENST00000888688.1		c.-227-125C>T	intron	N/A	ENSP00000558747.1
FGFBP1	ENST00000888689.1		c.-241-111C>T	intron	N/A	ENSP00000558748.1

Frequencies

GnomAD3 genomes

AF:

0.950

AC:

144525

AN:

152118

Hom.:

68755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.924

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.962

Gnomad ASJ

AF:

0.978

Gnomad EAS

AF:

0.815

Gnomad SAS

AF:

0.972

Gnomad FIN

AF:

0.987

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.954

GnomAD4 exome

AF:

0.974

AC:

226

AN:

232

Hom.:

110

Cov.:

AF XY:

0.984

AC XY:

124

AN XY:

126

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.988

AC:

170

AN:

172

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.957

AC:

AN:

Other (OTH)

AF:

0.917

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.950

AC:

144627

AN:

152236

Hom.:

68801

Cov.:

AF XY:

0.951

AC XY:

70783

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.924

AC:

38362

AN:

41534

American (AMR)

AF:

0.962

AC:

14720

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.978

AC:

3394

AN:

3472

East Asian (EAS)

AF:

0.814

AC:

4186

AN:

5140

South Asian (SAS)

AF:

0.973

AC:

4692

AN:

4824

European-Finnish (FIN)

AF:

0.987

AC:

10486

AN:

10626

Middle Eastern (MID)

AF:

0.969

AC:

285

AN:

294

European-Non Finnish (NFE)

AF:

0.964

AC:

65579

AN:

68024

Other (OTH)

AF:

0.952

AC:

2012

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

360

720

1079

1439

1799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<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:

0.962

Hom.:

35768

Bravo

AF:

0.947

Asia WGS

AF:

0.878

AC:

3053

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.52

(source)

DANN

Benign

0.28

PhyloP100

-0.69

PromoterAI

0.0082

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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