rs3829817

Positions:

• chr19-8096566-C-G
• chr19-8096566-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032447.5(FBN3):​c.5417G>C​(p.Arg1806Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1806Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: FBN3 NM_032447.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

FBN3 (HGNC:18794): (fibrillin 3) This gene encodes a memebr of the fibrillin protein family. Fibrillins are extracellular matrix molecules that assemble into microfibrils in many connective tissues. This gene is most highly expressed in fetal tissues and its protein product is localized to extracellular microfibrils of developing skeletal elements, skin, lung, kidney, and skeletal muscle. This gene is potentially involved in Weill-Marchesani syndrome. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBN3	NM_032447.5	c.5417G>C	p.Arg1806Pro	missense_variant	44/64	ENST00000600128.6	NP_115823.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBN3	ENST00000600128.6	c.5417G>C	p.Arg1806Pro	missense_variant	44/64	1	NM_032447.5	ENSP00000470498.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.030
CADD	Benign	18
DANN	Benign	0.93
DEOGEN2	Benign	0.18	T;T;T
Eigen	Benign	-0.89
Eigen_PC	Benign	-0.92
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.80	.;.;T
M_CAP	Benign	0.015	T
MetaRNN	Uncertain	0.56	D;D;D
MetaSVM	Benign	-0.57	T
MutationAssessor	Benign	1.6	L;L;L
PrimateAI	Benign	0.28	T
PROVEAN	Uncertain	-4.2	.;D;.
REVEL	Uncertain	0.48
Sift	Benign	0.14	.;T;.
Sift4G	Benign	0.15	T;T;T
Polyphen		0.0020	B;B;B
Vest4		0.28
MutPred		0.51		Loss of catalytic residue at R1806 (P = 0.0815);Loss of catalytic residue at R1806 (P = 0.0815);Loss of catalytic residue at R1806 (P = 0.0815);
MVP		0.64
MPC		0.37
ClinPred		0.61	D
GERP RS		-1.5
Varity_R		0.78
gMVP		0.85

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: rs3829817; hg19: chr19-8161450;