15-48572600-C-T

Position:

• chr15-48572600-C-T

Variant summary

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

The NM_000138.5(FBN1):​c.538+23683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 150,946 control chromosomes in the GnomAD database, including 2,840 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 0.19 (2840 hom., cov: 32)
• Consequence: FBN1 NM_000138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBN1	NM_000138.5	c.538+23683G>A		intron_variant		ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1	c.538+23683G>A		intron_variant			NP_001393645.1
FBN1	NM_001406717.1	c.538+23683G>A		intron_variant			NP_001393646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10	c.538+23683G>A		intron_variant		1	NM_000138.5	ENSP00000325527	P1
FBN1	ENST00000559133.6	c.538+23683G>A		intron_variant, NMD_transcript_variant		1		ENSP00000453958
FBN1	ENST00000537463.6	c.538+23683G>A		intron_variant, NMD_transcript_variant		5		ENSP00000440294
FBN1	ENST00000674301.2	c.538+23683G>A		intron_variant, NMD_transcript_variant				ENSP00000501333

Frequencies

GnomAD3 genomes AF: 0.192 AC: 28995 AN: 150864 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.192 AC: 29000 AN: 150946 Hom.: 2840 Cov.: 32 AF XY: 0.196 AC XY: 14430 AN XY: 73628

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.194

Alfa AF: 0.186 Hom.: 3725

Bravo AF: 0.184

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.69

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: rs12915677; hg19: chr15-48864797; COSMIC: COSV57310283;