rs9315120

Variant names:

• chr13-31249452-G-A
• rs9315120
• NM_194318.4:c.459+1486G>A

Variant summary

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

The NM_194318.4(B3GLCT):​c.459+1486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,000 control chromosomes in the GnomAD database, including 8,816 homozygotes. 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 0.32 (8816 hom., cov: 32)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661
• Publications: 7 publications found

Genes affected

B3GLCT (HGNC:20207): (beta 3-glucosyltransferase) The protein encoded by this gene is a beta-1,3-glucosyltransferase that transfers glucose to O-linked fucosylglycans on thrombospondin type-1 repeats (TSRs) of several proteins. The encoded protein is a type II membrane protein. Defects in this gene are a cause of Peters-plus syndrome (PPS).[provided by RefSeq, Mar 2009]

B3GLCT Gene-Disease associations (from GenCC):

• Peters plus syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet, G2P, PanelApp Australia

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194318.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	NM_194318.4	MANE Select	c.459+1486G>A		intron	N/A	NP_919299.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.459+1486G>A		intron	N/A	ENSP00000343002.4

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48385 AN: 151882 Hom.: 8817 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.325

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.318 AC: 48377 AN: 152000 Hom.: 8816 Cov.: 32 AF XY: 0.311 AC XY: 23113 AN XY: 74262

African (AFR) AF: 0.190 AC: 7898 AN: 41466

American (AMR) AF: 0.298 AC: 4549 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5188

South Asian (SAS) AF: 0.170 AC: 817 AN: 4814

European-Finnish (FIN) AF: 0.371 AC: 3904 AN: 10526

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28672 AN: 67956

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.386 Hom.: 51020

Bravo AF: 0.309

Asia WGS AF: 0.0890 AC: 312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		0.66
Mutation Taster		=100/0	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: rs9315120; hg19: chr13-31823589;