Variant 5-44310390-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004465.2(FGF10):c.429+37T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,383,974 control chromosomes in the GnomAD database, including 34,826 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3841 hom., cov: 32)

Exomes 𝑓: 0.22 ( 30985 hom. )

Consequence

FGF10
NM_004465.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.114

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]

FGF10 links:

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 5-44310390-A-T is Benign according to our data. Variant chr5-44310390-A-T is described in ClinVar as [Benign]. Clinvar id is 1270169.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2 linkuse as main transcript	c.429+37T>A		intron_variant		ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5 linkuse as main transcript	c.429+37T>A		intron_variant			XP_005248321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664.5 linkuse as main transcript	c.429+37T>A		intron_variant		1	NM_004465.2	ENSP00000264664	P1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33468

AN:

151980

Hom.:

3835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.242

AC:

58275

AN:

240730

Hom.:

8406

AF XY:

0.231

AC XY:

30001

AN XY:

130132

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.481

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.163

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.241

GnomAD4 exome

AF:

0.215

AC:

265093

AN:

1231876

Hom.:

30985

Cov.:

AF XY:

0.213

AC XY:

132908

AN XY:

624352

show subpopulations

Gnomad4 AFR exome

AF:

0.220

Gnomad4 AMR exome

AF:

0.463

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.192

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.206

Gnomad4 OTH exome

AF:

0.213

GnomAD4 genome

AF:

0.220

AC:

33512

AN:

152098

Hom.:

3841

Cov.:

AF XY:

0.218

AC XY:

16211

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.171

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.145

Hom.:

369

Bravo

AF:

0.232

Asia WGS

AF:

0.240

AC:

835

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 08, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.1

DANN

Benign

0.66

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over