Genetic Variant FGF14:c.*1387_*1390dupTAAA (chr13-101721440-C-CTTTA) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_004115.4(FGF14):c.*1387_*1390dupTAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.39 ( 11778 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

FGF14
NM_004115.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.02

Publications

1 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:

ENSG00000276012 (HGNC:):

ENSG00000276012 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP6

Variant 13-101721440-C-CTTTA is Benign according to our data. Variant chr13-101721440-C-CTTTA is described in ClinVar as [Benign]. Clinvar id is 310867.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF14	NM_004115.4 link	c.1387_1390dupTAAA		3_prime_UTR_variant	Exon 5 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.1387_1390dupTAAA		3_prime_UTR_variant	Exon 5 of 5	1	NM_004115.4	ENSP00000365313.4		Q92915-1

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58649

AN:

151368

Hom.:

11772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.405

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.387

AC:

58676

AN:

151486

Hom.:

11778

Cov.:

AF XY:

0.382

AC XY:

28291

AN XY:

73994

show subpopulations

African (AFR)

AF:

0.296

AC:

12223

AN:

41358

American (AMR)

AF:

0.357

AC:

5434

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

1500

AN:

3464

East Asian (EAS)

AF:

0.517

AC:

2628

AN:

5086

South Asian (SAS)

AF:

0.483

AC:

2313

AN:

4788

European-Finnish (FIN)

AF:

0.359

AC:

3768

AN:

10488

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.433

AC:

29320

AN:

67784

Other (OTH)

AF:

0.413

AC:

869

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1764

3528

5292

7056

8820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.394

Hom.:

1296

Asia WGS

AF:

0.528

AC:

1835

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Autosomal dominant cerebellar ataxia

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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13-101721440-C-CTTTA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over