rs2160079

Positions:

• chr14-91908061-A-C

Variant summary

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

The NM_006329.4(FBLN5):​c.380-12989T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,206 control chromosomes in the GnomAD database, including 56,841 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 0.86 (56841 hom., cov: 31)
• Consequence: FBLN5 NM_006329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

Genes affected

FBLN5 (HGNC:3602): (fibulin 5) The protein encoded by this gene is a secreted, extracellular matrix protein containing an Arg-Gly-Asp (RGD) motif and calcium-binding EGF-like domains. It promotes adhesion of endothelial cells through interaction of integrins and the RGD motif. It is prominently expressed in developing arteries but less so in adult vessels. However, its expression is reinduced in balloon-injured vessels and atherosclerotic lesions, notably in intimal vascular smooth muscle cells and endothelial cells. Therefore, the protein encoded by this gene may play a role in vascular development and remodeling. Defects in this gene are a cause of autosomal dominant cutis laxa, autosomal recessive cutis laxa type I (CL type I), and age-related macular degeneration type 3 (ARMD3). [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 (AMR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBLN5	NM_006329.4	c.380-12989T>G		intron_variant		ENST00000342058.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBLN5	ENST00000342058.9	c.380-12989T>G		intron_variant		1	NM_006329.4	P1

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130775 AN: 152088 Hom.: 56810 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.860 AC: 130870 AN: 152206 Hom.: 56841 Cov.: 31 AF XY: 0.859 AC XY: 63920 AN XY: 74390

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.883

Alfa AF: 0.889 Hom.: 33239

Bravo AF: 0.855

Asia WGS AF: 0.762 AC: 2652 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	4.7
DANN	Benign	0.65

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

LitVar

Other links and lift over

dbSNP: rs2160079; hg19: chr14-92374405;