rs11263592

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005247.4(FGF3):​c.324+1698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,884 control chromosomes in the GnomAD database, including 18,813 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 0.49 ( 18813 hom., cov: 31)

Consequence

FGF3
NM_005247.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGF3NM_005247.4 linkuse as main transcriptc.324+1698C>T intron_variant ENST00000334134.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGF3ENST00000334134.4 linkuse as main transcriptc.324+1698C>T intron_variant 1 NM_005247.4 P1
FGF3ENST00000646078.1 linkuse as main transcriptn.171+1698C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.494
AC:
75000
AN:
151766
Hom.:
18804
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.470
Gnomad AMI
AF:
0.714
Gnomad AMR
AF:
0.375
Gnomad ASJ
AF:
0.488
Gnomad EAS
AF:
0.617
Gnomad SAS
AF:
0.422
Gnomad FIN
AF:
0.612
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.511
Gnomad OTH
AF:
0.469
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.494
AC:
75042
AN:
151884
Hom.:
18813
Cov.:
31
AF XY:
0.495
AC XY:
36761
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.470
Gnomad4 AMR
AF:
0.375
Gnomad4 ASJ
AF:
0.488
Gnomad4 EAS
AF:
0.616
Gnomad4 SAS
AF:
0.422
Gnomad4 FIN
AF:
0.612
Gnomad4 NFE
AF:
0.511
Gnomad4 OTH
AF:
0.469
Alfa
AF:
0.510
Hom.:
3378
Bravo
AF:
0.478
Asia WGS
AF:
0.509
AC:
1770
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.5
DANN
Benign
0.43

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.

Other links and lift over

dbSNP: rs11263592; hg19: chr11-69629390; API