rs6819187

Variant summary

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

The NM_001361665.2(FGF2):​c.179-3306C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,106 control chromosomes in the GnomAD database, including 17,034 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 0.43 ( 17034 hom., cov: 33)

Consequence

FGF2
NM_001361665.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.297
Variant links:
Genes affected
FGF2 (HGNC:3676): (fibroblast growth factor 2) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members bind heparin and possess broad mitogenic and angiogenic activities. This protein has been implicated in diverse biological processes, such as limb and nervous system development, wound healing, and tumor growth. The mRNA for this gene contains multiple polyadenylation sites, and is alternatively translated from non-AUG (CUG) and AUG initiation codons, resulting in five different isoforms with distinct properties. The CUG-initiated isoforms are localized in the nucleus and are responsible for the intracrine effect, whereas, the AUG-initiated form is mostly cytosolic and is responsible for the paracrine and autocrine effects of this FGF. [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=-0.74).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGF2NM_001361665.2 linkuse as main transcriptc.179-3306C>A intron_variant ENST00000644866.2
FGF2NM_002006.6 linkuse as main transcriptc.578-3306C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGF2ENST00000644866.2 linkuse as main transcriptc.179-3306C>A intron_variant NM_001361665.2 P1P09038-2
FGF2ENST00000264498.9 linkuse as main transcriptc.578-3306C>A intron_variant 1 P09038-4
FGF2ENST00000608478.1 linkuse as main transcriptc.179-3306C>A intron_variant 1 P1P09038-2

Frequencies

GnomAD3 genomes
AF:
0.435
AC:
66097
AN:
151988
Hom.:
17029
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.618
Gnomad AMR
AF:
0.495
Gnomad ASJ
AF:
0.472
Gnomad EAS
AF:
0.494
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.598
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.573
Gnomad OTH
AF:
0.457
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.435
AC:
66117
AN:
152106
Hom.:
17034
Cov.:
33
AF XY:
0.432
AC XY:
32123
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.496
Gnomad4 ASJ
AF:
0.472
Gnomad4 EAS
AF:
0.493
Gnomad4 SAS
AF:
0.298
Gnomad4 FIN
AF:
0.598
Gnomad4 NFE
AF:
0.573
Gnomad4 OTH
AF:
0.459
Alfa
AF:
0.498
Hom.:
2550
Bravo
AF:
0.421
Asia WGS
AF:
0.421
AC:
1464
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
11
DANN
Benign
0.78

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: rs6819187; hg19: chr4-123794170; API