X-153504722-G-T

Variant names:

• chrX-153504722-G-T
• rs1011782727
• NM_001711.6:c.91G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001711.6(BGN):​c.91G>T​(p.Asp31Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,097,887 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D31N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: BGN NM_001711.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.06

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

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BGN	NM_001711.6	c.91G>T	p.Asp31Tyr	missense_variant	Exon 2 of 8	ENST00000331595.9	NP_001702.1
BGN	XM_017029724.3	c.91G>T	p.Asp31Tyr	missense_variant	Exon 1 of 7		XP_016885213.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BGN	ENST00000331595.9	c.91G>T	p.Asp31Tyr	missense_variant	Exon 2 of 8	1	NM_001711.6	ENSP00000327336.4
BGN	ENST00000431891.1	c.91G>T	p.Asp31Tyr	missense_variant	Exon 2 of 5	5		ENSP00000402525.1
BGN	ENST00000472615.5	n.235G>T		non_coding_transcript_exon_variant	Exon 2 of 8	5
BGN	ENST00000480756.1	n.233G>T		non_coding_transcript_exon_variant	Exon 2 of 8	5

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 9.11e-7 AC: 1 AN: 1097887 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 363333

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 26402

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 35206

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 19386

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 30206

Gnomad4 SAS exome AF: 0.0000185 AC: 1 AN: 54144

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 40314

Gnomad4 NFE exome AF: 0.00 AC: 0 AN: 842009

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 46085

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Jan 23, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 31 of the BGN protein (p.Asp31Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BGN-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Uncertain	0.075	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.31	T;T
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.85	T;D
M_CAP	Uncertain	0.17	D
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-0.39	T
MutationAssessor	Uncertain	2.5	M;.
PrimateAI	Uncertain	0.51	T
PROVEAN	Uncertain	-2.4	N;N
REVEL	Benign	0.23
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0040	D;D
Polyphen		0.98	D;.
Vest4		0.62
MutPred		0.52		Loss of disorder (P = 0.0393);Loss of disorder (P = 0.0393);
MVP		0.80
MPC		0.88
ClinPred		0.96	D
GERP RS		4.7
Varity_R		0.38
gMVP		0.75
Mutation Taster		=83/17	polymorphism

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: rs1011782727; hg19: chrX-152770180;