13-101868760-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1

The NM_004115.4(FGF14):c.373A>G(p.Ile125Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 1,613,526 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0013 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00015 ( 1 hom. )

Consequence

FGF14
NM_004115.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.21

Publications

3 publications found

Variant links:

Genes affected

FGF14 (HGNC:3671): (fibroblast growth factor 14) 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. A mutation in this gene is associated with autosomal dominant cerebral ataxia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

FGF14 Gene-Disease associations (from GenCC):

spinocerebellar ataxia 27A
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
spinocerebellar ataxia type 27
Inheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet
autosomal recessive cerebellar ataxia
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

FGF14 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013631076).

BP6

Variant 13-101868760-T-C is Benign according to our data. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-101868760-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 447326.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 = 0.00129 (197/152272) while in subpopulation AFR AF = 0.00445 (185/41566). AF 95% confidence interval is 0.00393. There are 1 homozygotes in GnomAd4. There are 81 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF14	NM_004115.4 link	c.373A>G	p.Ile125Val	missense_variant	Exon 3 of 5	ENST00000376143.5	NP_004106.1	Q92915-1A0A7U3JVZ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376143.5 link	c.373A>G	p.Ile125Val	missense_variant	Exon 3 of 5	1	NM_004115.4	ENSP00000365313.4		Q92915-1

Frequencies

GnomAD3 genomes

AF:

0.00131

AC:

199

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00449

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

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:

0.00

Gnomad OTH

AF:

0.00239

GnomAD2 exomes

AF:

0.000422

AC:

106

AN:

251402

AF XY:

0.000294

show subpopulations

Gnomad AFR exome

AF:

0.00535

Gnomad AMR exome

AF:

0.000405

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000176

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.000153

AC:

224

AN:

1461254

Hom.:

Cov.:

AF XY:

0.000142

AC XY:

103

AN XY:

726970

show subpopulations

African (AFR)

AF:

0.00466

AC:

156

AN:

33456

American (AMR)

AF:

0.000470

AC:

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26124

East Asian (EAS)

AF:

0.0000756

AC:

AN:

39676

South Asian (SAS)

AF:

0.0000348

AC:

AN:

86252

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.000520

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00000810

AC:

AN:

1111468

Other (OTH)

AF:

0.000480

AC:

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00129

AC:

197

AN:

152272

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00445

AC:

185

AN:

41566

American (AMR)

AF:

0.000458

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.00

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68022

Other (OTH)

AF:

0.00237

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000504

Hom.:

Bravo

AF:

0.00136

ESP6500AA

AF:

0.00340

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000502

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Jul 18, 2017

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Oct 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Uncertain

0.43

.;T

Eigen

Benign

-0.36

Eigen_PC

Benign

-0.097

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.81

T;T

MetaRNN

Benign

0.014

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.70

.;N

PhyloP100

1.2

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.42

N;N

REVEL

Benign

0.061

Sift

Benign

0.29

T;T

Sift4G

Benign

0.68

T;T

Polyphen

0.0010

B;B

Vest4

0.23

MVP

0.37

MPC

0.68

ClinPred

0.010

GERP RS

4.7

Varity_R

0.12

gMVP

0.37

Mutation Taster

=98/2

polymorphism

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over