Variant 11-65884359-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004214.5(FIBP):c.1004+33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 1,599,210 control chromosomes in the GnomAD database, including 505,149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.73 ( 41760 hom., cov: 31)

Exomes 𝑓: 0.80 ( 463389 hom. )

Consequence

FIBP
NM_004214.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.532

Variant links:

Genes affected

FIBP (HGNC:3705): (FGF1 intracellular binding protein) Acidic fibroblast growth factor is mitogenic for a variety of different cell types and acts by stimulating mitogenesis or inducing morphological changes and differentiation. The FIBP protein is an intracellular protein that binds selectively to acidic fibroblast growth factor (aFGF). It is postulated that FIBP may be involved in the mitogenic action of aFGF. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

FIBP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 11-65884359-A-G is Benign according to our data. Variant chr11-65884359-A-G is described in ClinVar as [Benign]. Clinvar id is 1285269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIBP	NM_004214.5 linkuse as main transcript	c.1004+33T>C		intron_variant		ENST00000357519.9
FIBP	NM_198897.2 linkuse as main transcript	c.1025+33T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIBP	ENST00000357519.9 linkuse as main transcript	c.1004+33T>C		intron_variant		1	NM_004214.5	P4	O43427-2

Frequencies

GnomAD3 genomes

AF:

0.730

AC:

110885

AN:

151910

Hom.:

41742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.886

Gnomad AMR

AF:

0.787

Gnomad ASJ

AF:

0.847

Gnomad EAS

AF:

0.569

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.836

Gnomad MID

AF:

0.807

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.741

GnomAD3 exomes

AF:

0.792

AC:

191360

AN:

241654

Hom.:

76891

AF XY:

0.802

AC XY:

104988

AN XY:

130914

show subpopulations

Gnomad AFR exome

AF:

0.545

Gnomad AMR exome

AF:

0.837

Gnomad ASJ exome

AF:

0.845

Gnomad EAS exome

AF:

0.560

Gnomad SAS exome

AF:

0.891

Gnomad FIN exome

AF:

0.839

Gnomad NFE exome

AF:

0.809

Gnomad OTH exome

AF:

0.804

GnomAD4 exome

AF:

0.798

AC:

1154666

AN:

1447180

Hom.:

463389

Cov.:

AF XY:

0.801

AC XY:

576861

AN XY:

720086

show subpopulations

Gnomad4 AFR exome

AF:

0.535

Gnomad4 AMR exome

AF:

0.829

Gnomad4 ASJ exome

AF:

0.843

Gnomad4 EAS exome

AF:

0.582

Gnomad4 SAS exome

AF:

0.887

Gnomad4 FIN exome

AF:

0.839

Gnomad4 NFE exome

AF:

0.803

Gnomad4 OTH exome

AF:

0.786

GnomAD4 genome

AF:

0.730

AC:

110931

AN:

152030

Hom.:

41760

Cov.:

AF XY:

0.735

AC XY:

54629

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.544

Gnomad4 AMR

AF:

0.787

Gnomad4 ASJ

AF:

0.847

Gnomad4 EAS

AF:

0.568

Gnomad4 SAS

AF:

0.882

Gnomad4 FIN

AF:

0.836

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.745

Alfa

AF:

0.775

Hom.:

9450

Bravo

AF:

0.719

Asia WGS

AF:

0.753

AC:

2618

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Tall stature-intellectual disability-renal anomalies syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.6

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over