X-153504296-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001711.6(BGN):c.-11-325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (10783 hom., 17147 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: BGN NM_001711.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.26

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant X-153504296-A-G is Benign according to our data. Variant chrX-153504296-A-G is described in ClinVar as [Benign]. Clinvar id is 1289069.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 10787 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BGN	NM_001711.6	c.-11-325A>G		intron_variant		ENST00000331595.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BGN	ENST00000331595.9	c.-11-325A>G		intron_variant		1	NM_001711.6	P1
BGN	ENST00000431891.1	c.-11-325A>G		intron_variant		5
BGN	ENST00000472615.5	n.134-325A>G		intron_variant, non_coding_transcript_variant		5
BGN	ENST00000480756.1	n.132-325A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 57160 AN: 111357 Hom.: 10787 Cov.: 24 AF XY: 0.510 AC XY: 17128 AN XY: 33583

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.515

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.476

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.513 AC: 57163 AN: 111413 Hom.: 10783 Cov.: 24 AF XY: 0.510 AC XY: 17147 AN XY: 33649

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.468

Alfa AF: 0.548 Hom.: 4148

Bravo AF: 0.490

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.58
Dann	Benign	0.41

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: rs2980051; hg19: chrX-152769754;