Variant chrX-153507015-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001711.6(BGN):c.771-32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,206,060 control chromosomes in the GnomAD database, including 61,626 homozygotes. There are 152,180 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 5326 hom., 12083 hem., cov: 23)

Exomes 𝑓: 0.39 ( 56300 hom. 140097 hem. )

Consequence

BGN
NM_001711.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.301

Variant links:

Genes affected

BGN (HGNC:1044): (biglycan) This gene encodes a member of the small leucine-rich proteoglycan (SLRP) family of proteins. The encoded preproprotein is proteolytically processed to generate the mature protein, which plays a role in bone growth, muscle development and regeneration, and collagen fibril assembly in multiple tissues. This protein may also regulate inflammation and innate immunity. Additionally, the encoded protein may contribute to atherosclerosis and aortic valve stenosis in human patients. This gene and the related gene decorin are thought to be the result of a gene duplication. [provided by RefSeq, Nov 2015]

BGN links:

BGN (HGNC:):

BGN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant X-153507015-C-T is Benign according to our data. Variant chrX-153507015-C-T is described in ClinVar as [Benign]. Clinvar id is 1192383.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BGN	NM_001711.6 linkuse as main transcript	c.771-32C>T		intron_variant		ENST00000331595.9	NP_001702.1	P21810B4DNL4
BGN	XM_017029724.3 linkuse as main transcript	c.771-32C>T		intron_variant			XP_016885213.1	P21810

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
BGN	ENST00000331595.9 linkuse as main transcript	c.771-32C>T	intron_variant	1	NM_001711.6	ENSP00000327336.4	P21810
BGN	ENST00000472615.5 linkuse as main transcript	n.788-32C>T	intron_variant	5
BGN	ENST00000480756.1 linkuse as main transcript	n.841-32C>T	intron_variant	5
BGN	ENST00000492658.1 linkuse as main transcript	n.294+401C>T	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

40363

AN:

111487

Hom.:

5321

Cov.:

AF XY:

0.358

AC XY:

12058

AN XY:

33717

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.483

Gnomad ASJ

AF:

0.466

Gnomad EAS

AF:

0.453

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.389

Gnomad MID

AF:

0.403

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.389

GnomAD3 exomes

AF:

0.408

AC:

73507

AN:

180058

Hom.:

10173

AF XY:

0.402

AC XY:

26089

AN XY:

64960

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.561

Gnomad ASJ exome

AF:

0.472

Gnomad EAS exome

AF:

0.420

Gnomad SAS exome

AF:

0.396

Gnomad FIN exome

AF:

0.388

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.426

GnomAD4 exome

AF:

0.388

AC:

425070

AN:

1094521

Hom.:

56300

Cov.:

AF XY:

0.389

AC XY:

140097

AN XY:

360359

show subpopulations

Gnomad4 AFR exome

AF:

0.263

Gnomad4 AMR exome

AF:

0.560

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.508

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.393

Gnomad4 NFE exome

AF:

0.377

Gnomad4 OTH exome

AF:

0.396

GnomAD4 genome

AF:

0.362

AC:

40387

AN:

111539

Hom.:

5326

Cov.:

AF XY:

0.358

AC XY:

12083

AN XY:

33779

show subpopulations

Gnomad4 AFR

AF:

0.259

Gnomad4 AMR

AF:

0.483

Gnomad4 ASJ

AF:

0.466

Gnomad4 EAS

AF:

0.453

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.389

Gnomad4 NFE

AF:

0.380

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.379

Hom.:

9796

Bravo

AF:

0.374

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 04, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

X-linked spondyloepimetaphyseal dysplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Meester-Loeys syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.9

DANN

Benign

0.80

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

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