13-101721164-TGAG-T

Variant summary

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

The NM_004115.4(FGF14):c.*1664_*1666del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0467 in 152,228 control chromosomes in the GnomAD database, including 209 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.047 (209 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: FGF14 NM_004115.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.44

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 13-101721164-TGAG-T is Benign according to our data. Variant chr13-101721164-TGAG-T is described in ClinVar as [Likely_benign]. Clinvar id is 310862.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF14	NM_004115.4	c.*1664_*1666del		3_prime_UTR_variant	5/5	ENST00000376143.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF14	ENST00000376143.5	c.*1664_*1666del		3_prime_UTR_variant	5/5	1	NM_004115.4	P2
FGF14	ENST00000376131.9	c.*1664_*1666del		3_prime_UTR_variant	5/5	1
	ENST00000415285.1	n.80-532_80-530del		intron_variant, non_coding_transcript_variant		3
FGF14	ENST00000706491.1	c.*2012_*2014del		3_prime_UTR_variant, NMD_transcript_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7094 AN: 152110 Hom.: 208 Cov.: 31

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0464

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0467 AC: 7105 AN: 152228 Hom.: 209 Cov.: 31 AF XY: 0.0471 AC XY: 3507 AN XY: 74424

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.0805

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.0615

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0478 Hom.: 29

Bravo AF: 0.0431

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autosomal dominant cerebellar ataxia Benign:1

Likely 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: rs141424596; hg19: chr13-102373514;