rs10057630

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004465.2(FGF10):​c.326-17232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,182 control chromosomes in the GnomAD database, including 2,750 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 0.12 ( 2750 hom., cov: 32)

Consequence

FGF10
NM_004465.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.554
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGF10NM_004465.2 linkuse as main transcriptc.326-17232A>G intron_variant ENST00000264664.5
FGF10XM_005248264.5 linkuse as main transcriptc.326-17232A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.326-17232A>G intron_variant 1 NM_004465.2 P1

Frequencies

GnomAD3 genomes
AF:
0.121
AC:
18417
AN:
152064
Hom.:
2749
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.0197
Gnomad AMR
AF:
0.0500
Gnomad ASJ
AF:
0.0257
Gnomad EAS
AF:
0.211
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.00640
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0193
Gnomad OTH
AF:
0.0903
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.121
AC:
18441
AN:
152182
Hom.:
2750
Cov.:
32
AF XY:
0.119
AC XY:
8851
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.347
Gnomad4 AMR
AF:
0.0499
Gnomad4 ASJ
AF:
0.0257
Gnomad4 EAS
AF:
0.211
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.00640
Gnomad4 NFE
AF:
0.0193
Gnomad4 OTH
AF:
0.0903
Alfa
AF:
0.0424
Hom.:
507
Bravo
AF:
0.135
Asia WGS
AF:
0.150
AC:
522
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
12
DANN
Benign
0.68

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: rs10057630; hg19: chr5-44327864; API