chrX-153508763-G-T

Position:

• chrX-153508763-G-T

Variant summary

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

The NM_001711.6(BGN):​c.*318G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 344,255 control chromosomes in the GnomAD database, including 5,549 homozygotes. There are 17,203 hemizygotes in GnomAD. 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 0.21 (2727 hom., 7112 hem., cov: 23)
  • Exomes 𝑓: 0.15 (2822 hom. 10091 hem.)
• Consequence: BGN NM_001711.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BGN	NM_001711.6	c.*318G>T		3_prime_UTR_variant	8/8	ENST00000331595.9	NP_001702.1
BGN	XM_017029724.3	c.*318G>T		3_prime_UTR_variant	7/7		XP_016885213.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BGN	ENST00000331595.9	c.*318G>T		3_prime_UTR_variant	8/8	1	NM_001711.6	ENSP00000327336.4
BGN	ENST00000472615.5	n.1442G>T		non_coding_transcript_exon_variant	8/8	5
BGN	ENST00000480756.1	n.1495G>T		non_coding_transcript_exon_variant	8/8	5
BGN	ENST00000492658.1	n.378G>T		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 23710 AN: 111297 Hom.: 2723 Cov.: 23 AF XY: 0.212 AC XY: 7101 AN XY: 33519

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.145 AC: 33827 AN: 232904 Hom.: 2822 Cov.: 0 AF XY: 0.160 AC XY: 10091 AN XY: 63074

Gnomad4 AFR exome AF: 0.387

Gnomad4 AMR exome AF: 0.457

Gnomad4 ASJ exome AF: 0.0377

Gnomad4 EAS exome AF: 0.305

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.0909

Gnomad4 NFE exome AF: 0.0876

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome AF: 0.213 AC: 23724 AN: 111351 Hom.: 2727 Cov.: 23 AF XY: 0.212 AC XY: 7112 AN XY: 33583

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.0909

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.236

Alfa AF: 0.103 Hom.: 3904

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.62

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: rs743642; hg19: chrX-152774221;