rs730880097

Variant names:

• chr15-48644769-T-A
• rs730880097
• NM_000138.5:c.1A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-48644769-T-A
• chr15-48644769-T-C
• chr15-48644769-T-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000138.5(FBN1):​c.1A>T​(p.Met1?) variant causes a initiator codon change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FBN1 NM_000138.5 initiator_codon
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.95

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 Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, next in-frame start position is after 13 pathogenic variants. Next in-frame start position is after 99 codons. Genomic position: 48610779. Lost 0.034 part of the original CDS.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 15-48644769-T-A is Pathogenic according to our data. Variant chr15-48644769-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 577426.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBN1	NM_000138.5	c.1A>T	p.Met1?	initiator_codon_variant	Exon 2 of 66	ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1	c.1A>T	p.Met1?	initiator_codon_variant	Exon 1 of 65		NP_001393645.1
FBN1	NM_001406717.1	c.1A>T	p.Met1?	initiator_codon_variant	Exon 2 of 9		NP_001393646.1
FBN1	NM_001406718.1	c.1A>T	p.Met1?	initiator_codon_variant	Exon 2 of 3		NP_001393647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10	c.1A>T	p.Met1?	initiator_codon_variant	Exon 2 of 66	1	NM_000138.5	ENSP00000325527.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1

Jun 27, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Cys89Tyr amino acid residue in FBN1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 19293843, 19720936; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 577426). Disruption of the initiator codon has been observed in individuals with Marfan syndrome (PMID: 19012347; 19159394. 27906200). This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the FBN1 mRNA. The next in-frame methionine is located at codon 99. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.30
CADD	Uncertain	23
DANN	Benign	0.93
DEOGEN2	Benign	0.33	.;T
Eigen	Benign	-0.024
Eigen_PC	Benign	0.097
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Pathogenic	0.77	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Benign	-0.44	T
PROVEAN	Benign	-0.50	N;N
REVEL	Uncertain	0.36
Sift	Benign	0.65	T;D
Sift4G	Benign	0.40	T;D
Vest4		0.85
MutPred		0.98		Loss of MoRF binding (P = 0.0662);Loss of MoRF binding (P = 0.0662);
MVP		0.97
ClinPred		0.93	D
GERP RS		4.6

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: rs730880097; hg19: chr15-48936966;