NM_032447.5:c.1929C>T

Variant names:

• chr19-8131615-G-A
• rs3813774
• NM_032447.5:c.1929C>T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_032447.5(FBN3):​c.1929C>T​(p.Cys643Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0715 in 1,614,004 control chromosomes in the GnomAD database, including 5,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (1087 hom., cov: 33)
  • Exomes 𝑓: 0.068 (4536 hom.)
• Consequence: FBN3 NM_032447.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 3.19

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 Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 19-8131615-G-A is Benign according to our data. Variant chr19-8131615-G-A is described in ClinVar as [Benign]. Clinvar id is 1288401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=3.19 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBN3	NM_032447.5	c.1929C>T	p.Cys643Cys	synonymous_variant	Exon 15 of 64	ENST00000600128.6	NP_115823.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN3	ENST00000600128.6	c.1929C>T	p.Cys643Cys	synonymous_variant	Exon 15 of 64	1	NM_032447.5	ENSP00000470498.1
FBN3	ENST00000270509.6	c.1929C>T	p.Cys643Cys	synonymous_variant	Exon 14 of 63	1		ENSP00000270509.2
FBN3	ENST00000601739.5	c.1929C>T	p.Cys643Cys	synonymous_variant	Exon 15 of 64	1		ENSP00000472324.1
FBN3	ENST00000651877.1	c.2055C>T	p.Cys685Cys	synonymous_variant	Exon 15 of 64			ENSP00000498507.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15311 AN: 152158 Hom.: 1087 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0980

GnomAD3 exomes AF: 0.0765 AC: 19208 AN: 251008 Hom.: 1168 AF XY: 0.0734 AC XY: 9960 AN XY: 135680

Gnomad AFR exome AF: 0.200

Gnomad AMR exome AF: 0.0459

Gnomad ASJ exome AF: 0.0598

Gnomad EAS exome AF: 0.222

Gnomad SAS exome AF: 0.0578

Gnomad FIN exome AF: 0.0269

Gnomad NFE exome AF: 0.0609

Gnomad OTH exome AF: 0.0699

GnomAD4 exome AF: 0.0685 AC: 100073 AN: 1461728 Hom.: 4536 Cov.: 65 AF XY: 0.0678 AC XY: 49301 AN XY: 727144

Gnomad4 AFR exome AF: 0.201

Gnomad4 AMR exome AF: 0.0487

Gnomad4 ASJ exome AF: 0.0548

Gnomad4 EAS exome AF: 0.245

Gnomad4 SAS exome AF: 0.0600

Gnomad4 FIN exome AF: 0.0294

Gnomad4 NFE exome AF: 0.0613

Gnomad4 OTH exome AF: 0.0742

GnomAD4 genome AF: 0.101 AC: 15330 AN: 152276 Hom.: 1087 Cov.: 33 AF XY: 0.0987 AC XY: 7349 AN XY: 74468

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0730 Hom.: 969

Bravo AF: 0.109

Asia WGS AF: 0.105 AC: 368 AN: 3478

EpiCase AF: 0.0654

EpiControl AF: 0.0715

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 14, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

FBN3-related disorder Benign:1

Oct 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	4.9
DANN	Benign	0.51

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: rs3813774; hg19: chr19-8196499; COSMIC: COSV54455857;