5-44304990-T-A

Variant summary

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

The NM_004465.2(FGF10):​c.*5A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 1,613,838 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 37 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 44 hom. )

Consequence

FGF10
NM_004465.2 3_prime_UTR

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.81
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=-0.56).
BP6
Variant 5-44304990-T-A is Benign according to our data. Variant chr5-44304990-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 369476.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1851/152330) while in subpopulation AFR AF= 0.0413 (1715/41564). AF 95% confidence interval is 0.0396. There are 37 homozygotes in gnomad4. There are 863 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1851 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FGF10NM_004465.2 linkuse as main transcriptc.*5A>T 3_prime_UTR_variant 3/3 ENST00000264664.5 NP_004456.1
FGF10XM_005248264.5 linkuse as main transcriptc.*5A>T 3_prime_UTR_variant 4/4 XP_005248321.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkuse as main transcriptc.*5A>T 3_prime_UTR_variant 3/31 NM_004465.2 ENSP00000264664 P1

Frequencies

GnomAD3 genomes
AF:
0.0120
AC:
1834
AN:
152212
Hom.:
33
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00412
Gnomad ASJ
AF:
0.0124
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00380
AC:
956
AN:
251346
Hom.:
20
AF XY:
0.00291
AC XY:
395
AN XY:
135836
show subpopulations
Gnomad AFR exome
AF:
0.0413
Gnomad AMR exome
AF:
0.00301
Gnomad ASJ exome
AF:
0.0133
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000246
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00159
AC:
2330
AN:
1461508
Hom.:
44
Cov.:
31
AF XY:
0.00143
AC XY:
1037
AN XY:
727052
show subpopulations
Gnomad4 AFR exome
AF:
0.0439
Gnomad4 AMR exome
AF:
0.00306
Gnomad4 ASJ exome
AF:
0.0119
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000899
Gnomad4 OTH exome
AF:
0.00464
GnomAD4 genome
AF:
0.0122
AC:
1851
AN:
152330
Hom.:
37
Cov.:
33
AF XY:
0.0116
AC XY:
863
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0413
Gnomad4 AMR
AF:
0.00412
Gnomad4 ASJ
AF:
0.0124
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00542
Hom.:
3
Bravo
AF:
0.0134
Asia WGS
AF:
0.00867
AC:
30
AN:
3476
EpiCase
AF:
0.000545
EpiControl
AF:
0.000178

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 12, 2021- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Congenital absence of salivary gland Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Levy-Hollister syndrome Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
5.5
DANN
Benign
0.67

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: rs111763965; hg19: chr5-44305092; API