Variant 11-69810617-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005247.4(FGF3):c.408G>A(p.Thr136Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 1,606,998 control chromosomes in the GnomAD database, including 7,926 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 559 hom., cov: 33)

Exomes 𝑓: 0.097 ( 7367 hom. )

Consequence

FGF3
NM_005247.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.11

Variant links:

Genes affected

FGF3 (HGNC:3681): (fibroblast growth factor 3) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members 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 gene was identified by its similarity with mouse fgf3/int-2, a proto-oncogene activated in virally induced mammary tumors in the mouse. Frequent amplification of this gene has been found in human tumors, which may be important for neoplastic transformation and tumor progression. Studies of the similar genes in mouse and chicken suggested the role in inner ear formation. [provided by RefSeq, Jul 2008]

FGF3 links:

FGF3 (HGNC:):

FGF3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 11-69810617-C-T is Benign according to our data. Variant chr11-69810617-C-T is described in ClinVar as [Benign]. Clinvar id is 259688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.11 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF3	NM_005247.4 linkuse as main transcript	c.408G>A	p.Thr136Thr	synonymous_variant	3/3	ENST00000334134.4	NP_005238.1	P11487A0A7U3JVY0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF3	ENST00000334134.4 linkuse as main transcript	c.408G>A	p.Thr136Thr	synonymous_variant	3/3	1	NM_005247.4	ENSP00000334122.2		P11487
FGF3	ENST00000646078.1 linkuse as main transcript	n.255G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes

AF:

0.0776

AC:

11809

AN:

152180

Hom.:

560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0437

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0425

Gnomad ASJ

AF:

0.0374

Gnomad EAS

AF:

0.0160

Gnomad SAS

AF:

0.0904

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0722

GnomAD3 exomes

AF:

0.0797

AC:

19721

AN:

247354

Hom.:

954

AF XY:

0.0821

AC XY:

11035

AN XY:

134328

show subpopulations

Gnomad AFR exome

AF:

0.0443

Gnomad AMR exome

AF:

0.0322

Gnomad ASJ exome

AF:

0.0346

Gnomad EAS exome

AF:

0.00982

Gnomad SAS exome

AF:

0.0896

Gnomad FIN exome

AF:

0.109

Gnomad NFE exome

AF:

0.106

Gnomad OTH exome

AF:

0.0787

GnomAD4 exome

AF:

0.0969

AC:

140892

AN:

1454700

Hom.:

7367

Cov.:

AF XY:

0.0970

AC XY:

70118

AN XY:

722628

show subpopulations

Gnomad4 AFR exome

AF:

0.0416

Gnomad4 AMR exome

AF:

0.0332

Gnomad4 ASJ exome

AF:

0.0376

Gnomad4 EAS exome

AF:

0.0169

Gnomad4 SAS exome

AF:

0.0921

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.106

Gnomad4 OTH exome

AF:

0.0810

GnomAD4 genome

AF:

0.0775

AC:

11806

AN:

152298

Hom.:

559

Cov.:

AF XY:

0.0775

AC XY:

5771

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0436

Gnomad4 AMR

AF:

0.0425

Gnomad4 ASJ

AF:

0.0374

Gnomad4 EAS

AF:

0.0160

Gnomad4 SAS

AF:

0.0909

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.0714

Alfa

AF:

0.0937

Hom.:

354

Bravo

AF:

0.0692

EpiCase

AF:

0.0949

EpiControl

AF:

0.0932

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 10, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

6.4

DANN

Benign

0.72

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