5-142613829-C-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000800.5(FGF1):​c.169+130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 960,512 control chromosomes in the GnomAD database, including 1,533 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 0.065 ( 850 hom., cov: 33)
Exomes 𝑓: 0.016 ( 683 hom. )

Consequence

FGF1
NM_000800.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

Publications

2 publications found
Variant links:
Genes affected
FGF1 (HGNC:3665): (fibroblast growth factor 1) 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 protein functions as a modifier of endothelial cell migration and proliferation, as well as an angiogenic factor. It acts as a mitogen for a variety of mesoderm- and neuroectoderm-derived cells in vitro, thus is thought to be involved in organogenesis. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
SPRY4-AS1 (HGNC:53465): (SPRY4 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGF1NM_000800.5 linkc.169+130G>T intron_variant Intron 2 of 3 ENST00000337706.7 NP_000791.1 P05230-1A0A7U3JVZ2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF1ENST00000337706.7 linkc.169+130G>T intron_variant Intron 2 of 3 2 NM_000800.5 ENSP00000338548.2 P05230-1

Frequencies

GnomAD3 genomes
AF:
0.0645
AC:
9806
AN:
152128
Hom.:
847
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0295
Gnomad ASJ
AF:
0.0173
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.0298
Gnomad FIN
AF:
0.00245
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.00484
Gnomad OTH
AF:
0.0444
GnomAD4 exome
AF:
0.0159
AC:
12824
AN:
808266
Hom.:
683
AF XY:
0.0155
AC XY:
6241
AN XY:
403936
show subpopulations
African (AFR)
AF:
0.197
AC:
3740
AN:
18960
American (AMR)
AF:
0.0210
AC:
396
AN:
18842
Ashkenazi Jewish (ASJ)
AF:
0.0140
AC:
214
AN:
15308
East Asian (EAS)
AF:
0.112
AC:
3576
AN:
31858
South Asian (SAS)
AF:
0.0246
AC:
1153
AN:
46826
European-Finnish (FIN)
AF:
0.00329
AC:
146
AN:
44416
Middle Eastern (MID)
AF:
0.0329
AC:
86
AN:
2612
European-Non Finnish (NFE)
AF:
0.00401
AC:
2376
AN:
592222
Other (OTH)
AF:
0.0305
AC:
1137
AN:
37222
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
551
1102
1653
2204
2755
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
206
412
618
824
1030
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0646
AC:
9831
AN:
152246
Hom.:
850
Cov.:
33
AF XY:
0.0637
AC XY:
4740
AN XY:
74460
show subpopulations
African (AFR)
AF:
0.193
AC:
8009
AN:
41506
American (AMR)
AF:
0.0294
AC:
450
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.0173
AC:
60
AN:
3470
East Asian (EAS)
AF:
0.135
AC:
698
AN:
5182
South Asian (SAS)
AF:
0.0296
AC:
143
AN:
4828
European-Finnish (FIN)
AF:
0.00245
AC:
26
AN:
10616
Middle Eastern (MID)
AF:
0.0748
AC:
22
AN:
294
European-Non Finnish (NFE)
AF:
0.00485
AC:
330
AN:
68022
Other (OTH)
AF:
0.0440
AC:
93
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
407
814
1220
1627
2034
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
102
204
306
408
510
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0164
Hom.:
33
Bravo
AF:
0.0722
Asia WGS
AF:
0.0900
AC:
314
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.7
DANN
Benign
0.64
PhyloP100
0.072
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs17217240; hg19: chr5-141993394; COSMIC: COSV107427764; COSMIC: COSV107427764; API