Variant 2-112165011-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_153214.3(FBLN7):c.246G>A(p.Pro82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,614,006 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 11 hom. )

Consequence

FBLN7
NM_153214.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.350

Variant links:

Genes affected

FBLN7 (HGNC:26740): (fibulin 7) Predicted to enable calcium ion binding activity; heparan sulfate proteoglycan binding activity; and heparin binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within positive regulation of biomineralization. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

FBLN7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 2-112165011-G-A is Benign according to our data. Variant chr2-112165011-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651270.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.35 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBLN7	NM_153214.3 linkuse as main transcript	c.246G>A	p.Pro82=	synonymous_variant	3/8	ENST00000331203.7	NP_694946.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBLN7	ENST00000331203.7 linkuse as main transcript	c.246G>A	p.Pro82=	synonymous_variant	3/8	1	NM_153214.3	ENSP00000331411	P1	Q53RD9-1

Frequencies

GnomAD3 genomes

AF:

0.00175

AC:

266

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000524

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00304

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00201

AC:

506

AN:

251168

Hom.:

AF XY:

0.00208

AC XY:

282

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.000782

Gnomad ASJ exome

AF:

0.00228

Gnomad EAS exome

AF:

0.000217

Gnomad SAS exome

AF:

0.00435

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.00256

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00271

AC:

3964

AN:

1461732

Hom.:

Cov.:

AF XY:

0.00275

AC XY:

2002

AN XY:

727158

show subpopulations

Gnomad4 AFR exome

AF:

0.000687

Gnomad4 AMR exome

AF:

0.000917

Gnomad4 ASJ exome

AF:

0.00253

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00481

Gnomad4 FIN exome

AF:

0.000468

Gnomad4 NFE exome

AF:

0.00291

Gnomad4 OTH exome

AF:

0.00230

GnomAD4 genome

AF:

0.00175

AC:

266

AN:

152274

Hom.:

Cov.:

AF XY:

0.00157

AC XY:

117

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00304

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00238

Hom.:

Bravo

AF:

0.00161

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00262

EpiControl

AF:

0.00184

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

FBLN7: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.55

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over