5-44305272-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004465.2(FGF10):​c.430-80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 1,302,442 control chromosomes in the GnomAD database, including 296 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 29 hom., cov: 33)
Exomes 𝑓: 0.019 ( 267 hom. )

Consequence

FGF10
NM_004465.2 intron

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0760
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 5-44305272-C-T is Benign according to our data. Variant chr5-44305272-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1183828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0146 (2215/152032) while in subpopulation NFE AF= 0.0234 (1591/68014). AF 95% confidence interval is 0.0224. There are 29 homozygotes in gnomad4. There are 1078 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2215 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FGF10NM_004465.2 linkuse as main transcriptc.430-80G>A intron_variant ENST00000264664.5 NP_004456.1
FGF10XM_005248264.5 linkuse as main transcriptc.430-80G>A intron_variant XP_005248321.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.430-80G>A intron_variant 1 NM_004465.2 ENSP00000264664 P1

Frequencies

GnomAD3 genomes
AF:
0.0146
AC:
2217
AN:
151914
Hom.:
29
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00348
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.00580
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00249
Gnomad FIN
AF:
0.0302
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0234
Gnomad OTH
AF:
0.0100
GnomAD4 exome
AF:
0.0192
AC:
22125
AN:
1150410
Hom.:
267
AF XY:
0.0188
AC XY:
11037
AN XY:
586474
show subpopulations
Gnomad4 AFR exome
AF:
0.00325
Gnomad4 AMR exome
AF:
0.00460
Gnomad4 ASJ exome
AF:
0.000249
Gnomad4 EAS exome
AF:
0.0000793
Gnomad4 SAS exome
AF:
0.00175
Gnomad4 FIN exome
AF:
0.0329
Gnomad4 NFE exome
AF:
0.0231
Gnomad4 OTH exome
AF:
0.0147
GnomAD4 genome
AF:
0.0146
AC:
2215
AN:
152032
Hom.:
29
Cov.:
33
AF XY:
0.0145
AC XY:
1078
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.00347
Gnomad4 AMR
AF:
0.00573
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00228
Gnomad4 FIN
AF:
0.0302
Gnomad4 NFE
AF:
0.0234
Gnomad4 OTH
AF:
0.00993
Alfa
AF:
0.0242
Hom.:
14
Bravo
AF:
0.0122
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingGeneDxApr 20, 2019- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
9.7
DANN
Benign
0.36

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: rs17228255; hg19: chr5-44305374; API