X-153504412-G-A

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.-11-209G>A 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 0.91 (32532 hom., 29898 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: BGN NM_001711.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.549

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=-0.91).
• BP6: Variant X-153504412-G-A is Benign according to our data. Variant chrX-153504412-G-A is described in ClinVar as [Benign]. Clinvar id is 1276181.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 32534 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BGN	NM_001711.6	c.-11-209G>A		intron_variant		ENST00000331595.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BGN	ENST00000331595.9	c.-11-209G>A		intron_variant		1	NM_001711.6	P1
BGN	ENST00000431891.1	c.-11-209G>A		intron_variant		5
BGN	ENST00000472615.5	n.134-209G>A		intron_variant, non_coding_transcript_variant		5
BGN	ENST00000480756.1	n.132-209G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.911 AC: 100729 AN: 110594 Hom.: 32534 Cov.: 23 AF XY: 0.910 AC XY: 29852 AN XY: 32802

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.971

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.942

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: 0.911 AC: 100766 AN: 110643 Hom.: 32532 Cov.: 23 AF XY: 0.910 AC XY: 29898 AN XY: 32861

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.942

Alfa AF: 0.926 Hom.: 7801

Bravo AF: 0.910

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

Mar 29, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.89
Dann	Benign	0.23

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: rs2980052; hg19: chrX-152769870;