rs17234079
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004465.2(FGF10):c.325+26256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,528 control chromosomes in the GnomAD database, including 1,617 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 0.13 ( 1617 hom., cov: 32)
Consequence
FGF10
NM_004465.2 intron
NM_004465.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.988
Publications
7 publications found
Genes affected
FGF10 (HGNC:3666): (fibroblast growth factor 10) 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 exhibits mitogenic activity for keratinizing epidermal cells, but essentially no activity for fibroblasts, which is similar to the biological activity of FGF7. Studies of the mouse homolog of suggested that this gene is required for embryonic epidermal morphogenesis including brain development, lung morphogenesis, and initiation of lim bud formation. This gene is also implicated to be a primary factor in the process of wound healing. [provided by RefSeq, Jul 2008]
FGF10 Gene-Disease associations (from GenCC):
- lacrimoauriculodentodigital syndrome 3Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- aplasia of lacrimal and salivary glandsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- LADD syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- congenital heart defects, multiple typesInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- craniosynostosisInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.325+26256C>T | intron_variant | Intron 1 of 2 | ENST00000264664.5 | NP_004456.1 | ||
FGF10 | XM_005248264.5 | c.325+26256C>T | intron_variant | Intron 2 of 3 | XP_005248321.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19706AN: 151410Hom.: 1618 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
19706
AN:
151410
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.130 AC: 19708AN: 151528Hom.: 1617 Cov.: 32 AF XY: 0.130 AC XY: 9611AN XY: 74030 show subpopulations
GnomAD4 genome
AF:
AC:
19708
AN:
151528
Hom.:
Cov.:
32
AF XY:
AC XY:
9611
AN XY:
74030
show subpopulations
African (AFR)
AF:
AC:
1282
AN:
41434
American (AMR)
AF:
AC:
2095
AN:
15182
Ashkenazi Jewish (ASJ)
AF:
AC:
732
AN:
3452
East Asian (EAS)
AF:
AC:
332
AN:
5108
South Asian (SAS)
AF:
AC:
952
AN:
4814
European-Finnish (FIN)
AF:
AC:
1618
AN:
10542
Middle Eastern (MID)
AF:
AC:
67
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12124
AN:
67684
Other (OTH)
AF:
AC:
318
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
871
1742
2614
3485
4356
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
224
448
672
896
1120
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
408
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.