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GeneBe

X-153504703-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001711.6(BGN):c.72C>G(p.Phe24Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,950 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 25)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

BGN
NM_001711.6 missense

Scores

1
3
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.840
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30996037).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BGNNM_001711.6 linkuse as main transcriptc.72C>G p.Phe24Leu missense_variant 2/8 ENST00000331595.9
BGNXM_017029724.3 linkuse as main transcriptc.72C>G p.Phe24Leu missense_variant 1/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BGNENST00000331595.9 linkuse as main transcriptc.72C>G p.Phe24Leu missense_variant 2/81 NM_001711.6 P1
BGNENST00000431891.1 linkuse as main transcriptc.72C>G p.Phe24Leu missense_variant 2/55
BGNENST00000472615.5 linkuse as main transcriptn.216C>G non_coding_transcript_exon_variant 2/85
BGNENST00000480756.1 linkuse as main transcriptn.214C>G non_coding_transcript_exon_variant 2/85

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD4 exome
AF:
9.11e-7
AC:
1
AN:
1097950
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
363398
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000119
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
25

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingBlueprint GeneticsJan 03, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.95
BayesDel_addAF
Benign
-0.067
T
BayesDel_noAF
Benign
-0.33
Cadd
Benign
17
Dann
Uncertain
1.0
DEOGEN2
Benign
0.15
T;T
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.77
T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.31
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.5
L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.17
Sift
Benign
0.62
T;T
Sift4G
Benign
0.64
T;T
Polyphen
0.046
B;.
Vest4
0.49
MutPred
0.44
Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
0.74
MPC
1.1
ClinPred
0.90
D
GERP RS
4.7
Varity_R
0.49
gMVP
0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-152770161; API