chr13-102211398-C-T

Position:

• chr13-102211398-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000376131.9(FGF14):​c.208+190073G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 151,924 control chromosomes in the GnomAD database, including 55,396 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 0.85 (55396 hom., cov: 34)
• Consequence: FGF14 ENST00000376131.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF14	NM_001321931.1	c.-300-18035G>A		intron_variant			NP_001308860.1
FGF14	NM_001321932.1	c.-323-18035G>A		intron_variant			NP_001308861.1
FGF14	NM_001321933.1	c.13+9299G>A		intron_variant			NP_001308862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF14	ENST00000376131.9	c.208+190073G>A		intron_variant		1		ENSP00000365301
FGF14	ENST00000418923.3	c.91+190073G>A		intron_variant		3		ENSP00000516414	A1
FGF14	ENST00000706494.1	c.-60+155047G>A		intron_variant				ENSP00000516417

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129126 AN: 151806 Hom.: 55354 Cov.: 34

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.851 AC: 129223 AN: 151924 Hom.: 55396 Cov.: 34 AF XY: 0.851 AC XY: 63150 AN XY: 74236

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.859

Alfa AF: 0.808 Hom.: 20577

Bravo AF: 0.857

Asia WGS AF: 0.847 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336698; hg19: chr13-102863748;