rs1876206

chr15-48608389-T-C

Variant summary

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

The NM_000138.5(FBN1):c.346+2339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,196 control chromosomes in the GnomAD database, including 1,289 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 0.12 (1289 hom., cov: 32)
• Consequence: FBN1 NM_000138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

FBN1 (HGNC:3603): (fibrillin 1) This gene encodes a member of the fibrillin family of proteins. The encoded preproprotein is proteolytically processed to generate two proteins including the extracellular matrix component fibrillin-1 and the protein hormone asprosin. Fibrillin-1 is an extracellular matrix glycoprotein that serves as a structural component of calcium-binding microfibrils. These microfibrils provide force-bearing structural support in elastic and nonelastic connective tissue throughout the body. Asprosin, secreted by white adipose tissue, has been shown to regulate glucose homeostasis. Mutations in this gene are associated with Marfan syndrome and the related MASS phenotype, as well as ectopia lentis syndrome, Weill-Marchesani syndrome, Shprintzen-Goldberg syndrome and neonatal progeroid syndrome. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBN1	NM_000138.5	c.346+2339A>G		intron_variant		ENST00000316623.10
FBN1	NM_001406716.1	c.346+2339A>G		intron_variant
FBN1	NM_001406717.1	c.346+2339A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBN1	ENST00000316623.10	c.346+2339A>G		intron_variant		1	NM_000138.5	P1
FBN1	ENST00000559133.6	c.346+2339A>G		intron_variant, NMD_transcript_variant		1
FBN1	ENST00000537463.6	c.346+2339A>G		intron_variant, NMD_transcript_variant		5
FBN1	ENST00000674301.2	c.346+2339A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18981 AN: 152078 Hom.: 1288 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0670

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.125 AC: 18999 AN: 152196 Hom.: 1289 Cov.: 32 AF XY: 0.127 AC XY: 9467 AN XY: 74408

Gnomad4 AFR AF: 0.0714

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0670

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.119

Alfa AF: 0.136 Hom.: 988

Bravo AF: 0.117

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.61
Dann	Benign	0.36

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: rs1876206; hg19: chr15-48900586;