5-44384121-C-T
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+4237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,072 control chromosomes in the GnomAD database, including 1,192 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 0.11 ( 1192 hom., cov: 32)
Consequence
FGF10
NM_004465.2 intron
NM_004465.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0220
Publications
4 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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.325+4237G>A | intron_variant | Intron 1 of 2 | ENST00000264664.5 | NP_004456.1 | ||
FGF10 | XM_005248264.5 | c.325+4237G>A | intron_variant | Intron 2 of 3 | XP_005248321.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.107 AC: 16324AN: 151954Hom.: 1193 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
16324
AN:
151954
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: 0.107 AC: 16316AN: 152072Hom.: 1192 Cov.: 32 AF XY: 0.102 AC XY: 7587AN XY: 74350 show subpopulations
GnomAD4 genome
AF:
AC:
16316
AN:
152072
Hom.:
Cov.:
32
AF XY:
AC XY:
7587
AN XY:
74350
show subpopulations
African (AFR)
AF:
AC:
1292
AN:
41530
American (AMR)
AF:
AC:
1925
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
539
AN:
3468
East Asian (EAS)
AF:
AC:
7
AN:
5188
South Asian (SAS)
AF:
AC:
238
AN:
4820
European-Finnish (FIN)
AF:
AC:
695
AN:
10590
Middle Eastern (MID)
AF:
AC:
44
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11039
AN:
67882
Other (OTH)
AF:
AC:
283
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
704
1408
2113
2817
3521
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
91
AN:
3470
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
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