3-31532766-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The ENST00000453168.5(STT3B):n.129A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 614,494 control chromosomes in the GnomAD database, including 12,250 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (2881 hom., cov: 33)
  • Exomes 𝑓: 0.20 (9369 hom.)
• Consequence: STT3B ENST00000453168.5 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0210

Genes affected

STT3B (HGNC:30611): (STT3 oligosaccharyltransferase complex catalytic subunit B) The protein encoded by this gene is a catalytic subunit of a protein complex that transfers oligosaccharides onto asparagine residues. Defects in this gene are a cause of congenital disorder of glycosylation Ix (CDG1X). [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 3-31532766-A-C is Benign according to our data. Variant chr3-31532766-A-C is described in ClinVar as [Benign]. Clinvar id is 1292289.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STT3B	ENST00000453168.5	n.129A>C		non_coding_transcript_exon_variant	1/10	1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28814 AN: 151704 Hom.: 2880 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.202

GnomAD4 exome AF: 0.199 AC: 92105 AN: 462670 Hom.: 9369 Cov.: 7 AF XY: 0.200 AC XY: 47312 AN XY: 237118

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.262

Gnomad4 ASJ exome AF: 0.233

Gnomad4 EAS exome AF: 0.311

Gnomad4 SAS exome AF: 0.181

Gnomad4 FIN exome AF: 0.193

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.190 AC: 28822 AN: 151824 Hom.: 2881 Cov.: 33 AF XY: 0.190 AC XY: 14080 AN XY: 74200

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.199

Alfa AF: 0.199 Hom.: 360

Bravo AF: 0.194

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	16
Dann	Benign	0.93
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs62234703; hg19: chr3-31574258;