5-44384121-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220

Publications

4 publications found
Variant links:
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 3
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
  • aplasia of lacrimal and salivary glands
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • LADD syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • congenital heart defects, multiple types
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
  • craniosynostosis
    Inheritance: 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
FGF10NM_004465.2 linkc.325+4237G>A intron_variant Intron 1 of 2 ENST00000264664.5 NP_004456.1 O15520A0A7U3JW18
FGF10XM_005248264.5 linkc.325+4237G>A intron_variant Intron 2 of 3 XP_005248321.1 O15520A0A7U3JW18

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkc.325+4237G>A intron_variant Intron 1 of 2 1 NM_004465.2 ENSP00000264664.4 O15520

Frequencies

GnomAD3 genomes
AF:
0.107
AC:
16324
AN:
151954
Hom.:
1193
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0312
Gnomad AMI
AF:
0.279
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0495
Gnomad FIN
AF:
0.0656
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.135
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.107
AC:
16316
AN:
152072
Hom.:
1192
Cov.:
32
AF XY:
0.102
AC XY:
7587
AN XY:
74350
show subpopulations
African (AFR)
AF:
0.0311
AC:
1292
AN:
41530
American (AMR)
AF:
0.126
AC:
1925
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.155
AC:
539
AN:
3468
East Asian (EAS)
AF:
0.00135
AC:
7
AN:
5188
South Asian (SAS)
AF:
0.0494
AC:
238
AN:
4820
European-Finnish (FIN)
AF:
0.0656
AC:
695
AN:
10590
Middle Eastern (MID)
AF:
0.150
AC:
44
AN:
294
European-Non Finnish (NFE)
AF:
0.163
AC:
11039
AN:
67882
Other (OTH)
AF:
0.134
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
178
356
534
712
890
<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:
0.127
Hom.:
788
Bravo
AF:
0.109
Asia WGS
AF:
0.0260
AC:
91
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.3
DANN
Benign
0.60
PhyloP100
-0.022
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: rs10512849; hg19: chr5-44384223; API