dbSNP rs3853818: FGF11:c.608-93T>C (chr17-7442983-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004112.4(FGF11):c.608-93T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,172,598 control chromosomes in the GnomAD database, including 166,920 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 17568 hom., cov: 31)

Exomes 𝑓: 0.52 ( 149352 hom. )

Consequence

FGF11
NM_004112.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Publications

19 publications found

Variant links:

Genes affected

FGF11 (HGNC:3667): (fibroblast growth factor 11) 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. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

FGF11 links:

ENSG00000272884 (HGNC:):

ENSG00000272884 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004112.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGF11	NM_004112.4	MANE Select	c.608-93T>C	intron	N/A	NP_004103.1	Q92914
FGF11	NM_001303460.2		c.431-93T>C	intron	N/A	NP_001290389.1	B7Z1C3
FGF11	NR_130156.2		n.648-93T>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FGF11	ENST00000293829.9	TSL:1 MANE Select	c.608-93T>C	intron	N/A	ENSP00000293829.4	Q92914
FGF11	ENST00000572907.5	TSL:1	c.236-93T>C	intron	N/A	ENSP00000465134.1	I3L4N4
FGF11	ENST00000575235.5	TSL:1	c.236-93T>C	intron	N/A	ENSP00000459746.1	I3L4N4

Frequencies

GnomAD3 genomes

AF:

0.462

AC:

70173

AN:

151834

Hom.:

17571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.675

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.0325

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.508

GnomAD4 exome

AF:

0.523

AC:

533550

AN:

1020646

Hom.:

149352

Cov.:

AF XY:

0.520

AC XY:

270786

AN XY:

520334

show subpopulations

African (AFR)

AF:

0.343

AC:

8422

AN:

24554

American (AMR)

AF:

0.293

AC:

11164

AN:

38080

Ashkenazi Jewish (ASJ)

AF:

0.584

AC:

11805

AN:

20214

East Asian (EAS)

AF:

0.0384

AC:

1446

AN:

37618

South Asian (SAS)

AF:

0.385

AC:

27015

AN:

70162

European-Finnish (FIN)

AF:

0.457

AC:

22967

AN:

50252

Middle Eastern (MID)

AF:

0.604

AC:

2868

AN:

4752

European-Non Finnish (NFE)

AF:

0.582

AC:

424805

AN:

729512

Other (OTH)

AF:

0.507

AC:

23058

AN:

45502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

12701

25402

38102

50803

63504

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9476

18952

28428

37904

47380

<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:

0.462

AC:

70180

AN:

151952

Hom.:

17568

Cov.:

AF XY:

0.451

AC XY:

33489

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.353

AC:

14628

AN:

41418

American (AMR)

AF:

0.394

AC:

6021

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.581

AC:

2014

AN:

3468

East Asian (EAS)

AF:

0.0326

AC:

169

AN:

5182

South Asian (SAS)

AF:

0.385

AC:

1857

AN:

4818

European-Finnish (FIN)

AF:

0.443

AC:

4671

AN:

10554

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.574

AC:

38966

AN:

67924

Other (OTH)

AF:

0.503

AC:

1063

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1819

3637

5456

7274

9093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<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:

0.552

Hom.:

38739

Bravo

AF:

0.454

Asia WGS

AF:

0.196

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.5

(source)

DANN

Benign

0.58

PhyloP100

0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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