rs11938826

Variant summary

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

The NM_001361665.2(FGF2):​c.178+24107C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,088 control chromosomes in the GnomAD database, including 11,272 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 0.30 ( 11272 hom., cov: 32)

Consequence

FGF2
NM_001361665.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FGF2NM_001361665.2 linkuse as main transcriptc.178+24107C>G intron_variant ENST00000644866.2 NP_001348594.1
FGF2NM_002006.6 linkuse as main transcriptc.577+24107C>G intron_variant NP_001997.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FGF2ENST00000644866.2 linkuse as main transcriptc.178+24107C>G intron_variant NM_001361665.2 ENSP00000494222 P1P09038-2
FGF2ENST00000264498.9 linkuse as main transcriptc.577+24107C>G intron_variant 1 ENSP00000264498 P09038-4
FGF2ENST00000608478.1 linkuse as main transcriptc.178+24107C>G intron_variant 1 ENSP00000477134 P1P09038-2

Frequencies

GnomAD3 genomes
AF:
0.305
AC:
46275
AN:
151970
Hom.:
11226
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.679
Gnomad AMI
AF:
0.0757
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.160
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.222
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.157
Gnomad OTH
AF:
0.272
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.305
AC:
46375
AN:
152088
Hom.:
11272
Cov.:
32
AF XY:
0.299
AC XY:
22249
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.679
Gnomad4 AMR
AF:
0.222
Gnomad4 ASJ
AF:
0.160
Gnomad4 EAS
AF:
0.135
Gnomad4 SAS
AF:
0.220
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.157
Gnomad4 OTH
AF:
0.271
Alfa
AF:
0.238
Hom.:
971
Bravo
AF:
0.332
Asia WGS
AF:
0.253
AC:
878
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.59
DANN
Benign
0.40

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: rs11938826; hg19: chr4-123772614; API