Variant 8-22043246-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_003867.4(FGF17):c.72+65A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 1,533,786 control chromosomes in the GnomAD database, including 117,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 14889 hom., cov: 33)

Exomes 𝑓: 0.38 ( 102670 hom. )

Consequence

FGF17
NM_003867.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.24

Variant links:

Genes affected

FGF17 (HGNC:3673): (fibroblast growth factor 17) This gene encodes a member of the fibroblast growth factor (FGF) family. Member of the FGF family possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes including embryonic development cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein is expressed during embryogenesis and in the adult cerebellum and cortex and may be essential for vascular growth and normal brain development. Mutations in this gene are the cause of hypogonadotropic hypogonadism 20 with or without anosmia. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

FGF17 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=-0.82).

BP6

Variant 8-22043246-A-G is Benign according to our data. Variant chr8-22043246-A-G is described in ClinVar as [Benign]. Clinvar id is 1248234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF17	NM_003867.4 linkuse as main transcript	c.72+65A>G		intron_variant		ENST00000359441.4	NP_003858.1	O60258-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF17	ENST00000359441.4 linkuse as main transcript	c.72+65A>G		intron_variant		1	NM_003867.4	ENSP00000352414.3		O60258-1
FGF17	ENST00000518533.5 linkuse as main transcript	c.72+65A>G		intron_variant		1		ENSP00000431041.1		O60258-2

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65339

AN:

151850

Hom.:

14847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.567

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.382

AC:

527591

AN:

1381816

Hom.:

102670

AF XY:

0.382

AC XY:

263445

AN XY:

690350

show subpopulations

Gnomad4 AFR exome

AF:

0.578

Gnomad4 AMR exome

AF:

0.298

Gnomad4 ASJ exome

AF:

0.351

Gnomad4 EAS exome

AF:

0.584

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.407

Gnomad4 NFE exome

AF:

0.369

Gnomad4 OTH exome

AF:

0.402

GnomAD4 genome

AF:

0.431

AC:

65436

AN:

151970

Hom.:

14889

Cov.:

AF XY:

0.430

AC XY:

31925

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.568

Gnomad4 AMR

AF:

0.327

Gnomad4 ASJ

AF:

0.339

Gnomad4 EAS

AF:

0.622

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.367

Gnomad4 OTH

AF:

0.412

Alfa

AF:

0.382

Hom.:

2225

Bravo

AF:

0.431

Asia WGS

AF:

0.528

AC:

1836

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.0

DANN

Benign

0.57

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

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