chr5-44310390-A-T

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

2

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]

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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
FGF10NM_004465.2 linkuse as main transcriptc.429+37T>A intron_variant ENST00000264664.5 NP_004456.1
FGF10XM_005248264.5 linkuse as main transcriptc.429+37T>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.429+37T>A intron_variant 1 NM_004465.2 ENSP00000264664 P1

Frequencies

GnomAD3 genomes
AF:
0.220
AC:
33468
AN:
151980
Hom.:
3835
Cov.:
32
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.:
16
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.:
32
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 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.

Other links and lift over

dbSNP: rs6881797; hg19: chr5-44310492; COSMIC: COSV52933040; API