Genetic Variant FGF10:c.-294delG (chr5-44388975-TC-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004465.2(FGF10):c.-294delG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 538,012 control chromosomes in the GnomAD database, including 241 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 189 hom., cov: 31)

Exomes 𝑓: 0.0038 ( 52 hom. )

Consequence

FGF10
NM_004465.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.276

Publications

1 publications found

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:

FGF10-AS1 (HGNC:49382): (FGF10 antisense RNA 1)

FGF10-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 5-44388975-TC-T is Benign according to our data. Variant chr5-44388975-TC-T is described in ClinVar as Benign. ClinVar VariationId is 1236153.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004465.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF10	NM_004465.2	MANE Select	c.-294delG		5_prime_UTR	Exon 1 of 3	NP_004456.1	O15520
	FGF10-AS1	NR_108034.1		n.182+63delC		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGF10	ENST00000264664.5	TSL:1 MANE Select	c.-294delG	5_prime_UTR	Exon 1 of 3	ENSP00000264664.4	O15520
FGF10-AS1	ENST00000502457.1	TSL:1	n.182+63delC	intron	N/A
FGF10	ENST00000912799.1		c.-294delG	5_prime_UTR	Exon 2 of 4	ENSP00000582858.1

Frequencies

GnomAD3 genomes

AF:

0.0271

AC:

4123

AN:

152148

Hom.:

189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0921

Gnomad AMI

AF:

0.0407

Gnomad AMR

AF:

0.0138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.0220

GnomAD4 exome

AF:

0.00381

AC:

1470

AN:

385746

Hom.:

Cov.:

AF XY:

0.00313

AC XY:

638

AN XY:

203832

show subpopulations

African (AFR)

AF:

0.0969

AC:

1083

AN:

11176

American (AMR)

AF:

0.00749

AC:

125

AN:

16686

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11784

East Asian (EAS)

AF:

0.00

AC:

AN:

25190

South Asian (SAS)

AF:

0.000339

AC:

AN:

44264

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23384

Middle Eastern (MID)

AF:

0.00409

AC:

AN:

1710

European-Non Finnish (NFE)

AF:

0.000266

AC:

AN:

229158

Other (OTH)

AF:

0.00799

AC:

179

AN:

22394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

152

229

305

381

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0271

AC:

4130

AN:

152266

Hom.:

189

Cov.:

AF XY:

0.0269

AC XY:

2006

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0919

AC:

3819

AN:

41538

American (AMR)

AF:

0.0138

AC:

211

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.000414

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000221

AC:

AN:

68014

Other (OTH)

AF:

0.0218

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

193

387

580

774

967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00111

Hom.:

Bravo

AF:

0.0317

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over