13-101721440-C-CTTTA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004115.4(FGF14):c.*1390_*1391insTAAA 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FGF14	NM_004115.4	c.*1390_*1391insTAAA		3_prime_UTR_variant	5/5	ENST00000376143.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF14	ENST00000376143.5	c.*1390_*1391insTAAA		3_prime_UTR_variant	5/5	1	NM_004115.4	P2
FGF14	ENST00000376131.9	c.*1390_*1391insTAAA		3_prime_UTR_variant	5/5	1
	ENST00000415285.1	n.80-253_80-250dup		intron_variant, non_coding_transcript_variant		3
FGF14	ENST00000706491.1	c.*1738_*1739insTAAA		3_prime_UTR_variant, NMD_transcript_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58649 AN: 151368 Hom.: 11772 Cov.: 0

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: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.387 AC: 58676 AN: 151486 Hom.: 11778 Cov.: 0 AF XY: 0.382 AC XY: 28291 AN XY: 73994

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.413

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

Submissions by phenotype

Autosomal dominant cerebellar ataxia Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10626847; hg19: chr13-102373790;