NM_001711.6:c.-51G>T

Variant names:

• chrX-153495074-G-T
• rs5945197
• NM_001711.6:c.-51G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001711.6(BGN):​c.-51G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 108,973 control chromosomes in the GnomAD database, including 4,714 homozygotes. There are 9,480 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 0.31 (4708 hom., 9448 hem., cov: 21)
  • Exomes 𝑓: 0.45 (6 hom. 32 hem.)
• Consequence: BGN NM_001711.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 5 publications found

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]

HAUS7 (HGNC:32979): (HAUS augmin like complex subunit 7) This gene encodes a subunit of the augmin complex, which regulates centrosome and mitotic spindle integrity, and is necessary for the completion of cytokinesis. The encoded protein was identified by interaction with ubiquitin C-terminal hydrolase 37. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001711.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BGN	NM_001711.6	MANE Select	c.-51G>T		5_prime_UTR	Exon 1 of 8	NP_001702.1
	HAUS7	NM_001385483.1		c.-589+300C>A		intron	N/A	NP_001372412.1
	HAUS7	NR_073156.2		n.92+300C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BGN	ENST00000331595.9	TSL:1 MANE Select	c.-51G>T		5_prime_UTR	Exon 1 of 8	ENSP00000327336.4
	BGN	ENST00000859733.1		c.-51G>T		5_prime_UTR	Exon 1 of 9	ENSP00000529792.1
	BGN	ENST00000859723.1		c.-51G>T		5_prime_UTR	Exon 2 of 9	ENSP00000529782.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 34203 AN: 108792 Hom.: 4709 Cov.: 21

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.448 AC: 60 AN: 134 Hom.: 6 Cov.: 0 AF XY: 0.471 AC XY: 32 AN XY: 68

African (AFR) AF: 0.00 AC: 0 AN: 7

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 10

European-Finnish (FIN) AF: 0.583 AC: 7 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1

European-Non Finnish (NFE) AF: 0.549 AC: 50 AN: 91

Other (OTH) AF: 0.273 AC: 3 AN: 11

GnomAD4 genome AF: 0.314 AC: 34195 AN: 108839 Hom.: 4708 Cov.: 21 AF XY: 0.302 AC XY: 9448 AN XY: 31279

African (AFR) AF: 0.150 AC: 4497 AN: 29925

American (AMR) AF: 0.217 AC: 2242 AN: 10354

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1146 AN: 2603

East Asian (EAS) AF: 0.107 AC: 371 AN: 3457

South Asian (SAS) AF: 0.201 AC: 496 AN: 2462

European-Finnish (FIN) AF: 0.428 AC: 2408 AN: 5621

Middle Eastern (MID) AF: 0.301 AC: 65 AN: 216

European-Non Finnish (NFE) AF: 0.429 AC: 22323 AN: 52065

Other (OTH) AF: 0.293 AC: 432 AN: 1474

Alfa AF: 0.314 Hom.: 2683

Bravo AF: 0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.0
DANN	Benign	0.88
PhyloP100		1.9
PromoterAI		0.050	Neutral
Mutation Taster		=298/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5945197; hg19: chrX-152760532;