chr5-44305283-TTC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004465.2(FGF10):​c.430-93_430-92del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00927 in 1,210,706 control chromosomes in the GnomAD database, including 458 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.013 ( 86 hom., cov: 32)
Exomes 𝑓: 0.0087 ( 372 hom. )

Consequence

FGF10
NM_004465.2 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.750
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 5-44305283-TTC-T is Benign according to our data. Variant chr5-44305283-TTC-T is described in ClinVar as [Likely_benign]. Clinvar id is 1191155.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FGF10NM_004465.2 linkuse as main transcriptc.430-93_430-92del intron_variant ENST00000264664.5 NP_004456.1
FGF10XM_005248264.5 linkuse as main transcriptc.430-93_430-92del intron_variant XP_005248321.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.430-93_430-92del intron_variant 1 NM_004465.2 ENSP00000264664 P1

Frequencies

GnomAD3 genomes
AF:
0.0132
AC:
2010
AN:
152168
Hom.:
86
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00166
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0593
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.118
Gnomad SAS
AF:
0.0124
Gnomad FIN
AF:
0.0234
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00123
Gnomad OTH
AF:
0.0153
GnomAD4 exome
AF:
0.00870
AC:
9210
AN:
1058420
Hom.:
372
AF XY:
0.00834
AC XY:
4533
AN XY:
543412
show subpopulations
Gnomad4 AFR exome
AF:
0.00160
Gnomad4 AMR exome
AF:
0.0554
Gnomad4 ASJ exome
AF:
0.0000426
Gnomad4 EAS exome
AF:
0.116
Gnomad4 SAS exome
AF:
0.00993
Gnomad4 FIN exome
AF:
0.0169
Gnomad4 NFE exome
AF:
0.000601
Gnomad4 OTH exome
AF:
0.0121
GnomAD4 genome
AF:
0.0132
AC:
2017
AN:
152286
Hom.:
86
Cov.:
32
AF XY:
0.0165
AC XY:
1226
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.00166
Gnomad4 AMR
AF:
0.0596
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.118
Gnomad4 SAS
AF:
0.0124
Gnomad4 FIN
AF:
0.0234
Gnomad4 NFE
AF:
0.00123
Gnomad4 OTH
AF:
0.0161
Alfa
AF:
0.00556
Hom.:
4
Bravo
AF:
0.0145
Asia WGS
AF:
0.0860
AC:
298
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 testingGeneDxMar 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: rs17228248; hg19: chr5-44305385; API