rs1482672

Variant summary

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

The NM_004465.2(FGF10):​c.325+25691G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,314 control chromosomes in the GnomAD database, including 23,759 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 0.54 ( 23759 hom., cov: 31)

Consequence

FGF10
NM_004465.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FGF10NM_004465.2 linkuse as main transcriptc.325+25691G>A intron_variant ENST00000264664.5 NP_004456.1 O15520A0A7U3JW18
FGF10XM_005248264.5 linkuse as main transcriptc.325+25691G>A intron_variant XP_005248321.1 O15520A0A7U3JW18

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.325+25691G>A intron_variant 1 NM_004465.2 ENSP00000264664.4 O15520

Frequencies

GnomAD3 genomes
AF:
0.536
AC:
80997
AN:
151196
Hom.:
23760
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.653
Gnomad AMR
AF:
0.476
Gnomad ASJ
AF:
0.665
Gnomad EAS
AF:
0.491
Gnomad SAS
AF:
0.608
Gnomad FIN
AF:
0.662
Gnomad MID
AF:
0.601
Gnomad NFE
AF:
0.670
Gnomad OTH
AF:
0.561
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.535
AC:
81009
AN:
151314
Hom.:
23759
Cov.:
31
AF XY:
0.538
AC XY:
39735
AN XY:
73892
show subpopulations
Gnomad4 AFR
AF:
0.286
Gnomad4 AMR
AF:
0.475
Gnomad4 ASJ
AF:
0.665
Gnomad4 EAS
AF:
0.493
Gnomad4 SAS
AF:
0.609
Gnomad4 FIN
AF:
0.662
Gnomad4 NFE
AF:
0.670
Gnomad4 OTH
AF:
0.555
Alfa
AF:
0.601
Hom.:
8614
Bravo
AF:
0.508
Asia WGS
AF:
0.467
AC:
1624
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
4.0
DANN
Benign
0.51

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: rs1482672; hg19: chr5-44362769; COSMIC: COSV52935510; API