Genetic Variant FGF16:c.378+41_378+42dupTT (chrX-77454272-G-GTT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003868.3(FGF16):c.378+41_378+42dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.061 ( 452 hom., 157 hem., cov: 11)

Exomes 𝑓: 0.058 ( 3 hom. 57 hem. )

Failed GnomAD Quality Control

Consequence

FGF16
NM_003868.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.691

Publications

0 publications found

Variant links:

Genes affected

FGF16 (HGNC:3672): (fibroblast growth factor 16) This gene encodes a member of a family of proteins that are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This gene is expressed in cardiac cells and is required for proper heart development. Mutation in this gene was also observed in individuals with metacarpal 4-5 fusion. [provided by RefSeq, Mar 2014]

FGF16 Gene-Disease associations (from GenCC):

syndactyly type 8
Inheritance: AD, XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

FGF16 links:

ENSG00000295984 (HGNC:):

ENSG00000295984 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003868.3. 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
	FGF16	NM_003868.3	MANE Select	c.378+41_378+42dupTT		intron	N/A	NP_003859.1	O43320

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGF16	ENST00000439435.3	TSL:1 MANE Select	c.378+12_378+13insTT	intron	N/A	ENSP00000399324.2	O43320
ENSG00000295984	ENST00000734738.1		n.179+6933_179+6934insAA	intron	N/A
ENSG00000295984	ENST00000734739.1		n.45+6933_45+6934insAA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0610

AC:

2802

AN:

45907

Hom.:

452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0598

Gnomad AMI

AF:

0.0245

Gnomad AMR

AF:

0.0293

Gnomad ASJ

AF:

0.0470

Gnomad EAS

AF:

0.0191

Gnomad SAS

AF:

0.0185

Gnomad FIN

AF:

0.0170

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0723

Gnomad OTH

AF:

0.0385

GnomAD2 exomes

AF:

0.0164

AC:

388

AN:

23700

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.0277

Gnomad AMR exome

AF:

0.0395

Gnomad ASJ exome

AF:

0.0130

Gnomad EAS exome

AF:

0.0554

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0123

Gnomad OTH exome

AF:

0.0262

GnomAD4 exome

AF:

0.0582

AC:

5808

AN:

99754

Hom.:

Cov.:

AF XY:

0.00223

AC XY:

AN XY:

25536

show subpopulations

African (AFR)

AF:

0.0637

AC:

AN:

1460

American (AMR)

AF:

0.0475

AC:

154

AN:

3244

Ashkenazi Jewish (ASJ)

AF:

0.0488

AC:

139

AN:

2849

East Asian (EAS)

AF:

0.0490

AC:

107

AN:

2185

South Asian (SAS)

AF:

0.0511

AC:

607

AN:

11870

European-Finnish (FIN)

AF:

0.0262

AC:

387

AN:

14752

Middle Eastern (MID)

AF:

0.0427

AC:

AN:

445

European-Non Finnish (NFE)

AF:

0.0687

AC:

3996

AN:

58179

Other (OTH)

AF:

0.0642

AC:

306

AN:

4770

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.402

Heterozygous variant carriers

208

416

623

831

1039

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0610

AC:

2802

AN:

45902

Hom.:

452

Cov.:

AF XY:

0.0173

AC XY:

157

AN XY:

9060

show subpopulations

African (AFR)

AF:

0.0597

AC:

595

AN:

9959

American (AMR)

AF:

0.0293

AC:

107

AN:

3652

Ashkenazi Jewish (ASJ)

AF:

0.0470

AC:

AN:

1427

East Asian (EAS)

AF:

0.0192

AC:

AN:

1196

South Asian (SAS)

AF:

0.0184

AC:

AN:

544

European-Finnish (FIN)

AF:

0.0170

AC:

AN:

1179

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0723

AC:

1949

AN:

26946

Other (OTH)

AF:

0.0384

AC:

AN:

573

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.617

Heterozygous variant carriers

126

190

253

316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0151

Hom.:

186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.69

Splicing

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

Publications

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X-77454272-GTTTTTTTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTTTT

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