5-44310216-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_004465.2(FGF10):​c.429+210del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00912 in 152,210 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0091 ( 14 hom., cov: 32)

Consequence

FGF10
NM_004465.2 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.01
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 5-44310216-TG-T is Benign according to our data. Variant chr5-44310216-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201459.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00912 (1388/152210) while in subpopulation NFE AF= 0.0127 (867/68008). AF 95% confidence interval is 0.012. There are 14 homozygotes in gnomad4. There are 681 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1388 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGF10NM_004465.2 linkuse as main transcriptc.429+210del intron_variant ENST00000264664.5
FGF10XM_005248264.5 linkuse as main transcriptc.429+210del intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.429+210del intron_variant 1 NM_004465.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00913
AC:
1388
AN:
152092
Hom.:
14
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00208
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00492
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.000773
Gnomad SAS
AF:
0.00704
Gnomad FIN
AF:
0.0283
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0127
Gnomad OTH
AF:
0.00720
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00912
AC:
1388
AN:
152210
Hom.:
14
Cov.:
32
AF XY:
0.00915
AC XY:
681
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.00207
Gnomad4 AMR
AF:
0.00491
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.000775
Gnomad4 SAS
AF:
0.00705
Gnomad4 FIN
AF:
0.0283
Gnomad4 NFE
AF:
0.0127
Gnomad4 OTH
AF:
0.00712
Alfa
AF:
0.0105
Hom.:
2
Bravo
AF:
0.00693
Asia WGS
AF:
0.00346
AC:
12
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxAug 06, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs577957727; hg19: chr5-44310318; API