chr3-31532766-A-C

Variant names:

• chr3-31532766-A-C
• rs62234703
• ENST00000453168.5:n.129A>C

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The ENST00000935233.1(STT3B):​c.-233A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 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 ENST00000935233.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0210
• Publications: 0 publications found

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]

STT3B Gene-Disease associations (from GenCC):

• STT3B-congenital disorder of glycosylation

  Inheritance: AR, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: G2P, PanelApp Australia, Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000288926 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -18 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 VariationId is 1292289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000935233.1. 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
	STT3B	NM_178862.3	MANE Select	c.-233A>C		upstream_gene	N/A	NP_849193.1	Q8TCJ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STT3B	ENST00000453168.5	TSL:1	n.129A>C		non_coding_transcript_exon	Exon 1 of 10
	STT3B	ENST00000935233.1		c.-233A>C		5_prime_UTR	Exon 1 of 16	ENSP00000605292.1
	STT3B	ENST00000868023.1		c.-233A>C		5_prime_UTR	Exon 1 of 15	ENSP00000538082.1

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

African (AFR) AF: 0.152 AC: 1536 AN: 10134

American (AMR) AF: 0.262 AC: 2157 AN: 8246

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 2663 AN: 11420

East Asian (EAS) AF: 0.311 AC: 7358 AN: 23632

South Asian (SAS) AF: 0.181 AC: 5412 AN: 29880

European-Finnish (FIN) AF: 0.193 AC: 4920 AN: 25478

Middle Eastern (MID) AF: 0.250 AC: 447 AN: 1788

European-Non Finnish (NFE) AF: 0.191 AC: 62785 AN: 327890

Other (OTH) AF: 0.199 AC: 4827 AN: 24202

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

African (AFR) AF: 0.155 AC: 6412 AN: 41426

American (AMR) AF: 0.243 AC: 3718 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3462

East Asian (EAS) AF: 0.264 AC: 1347 AN: 5104

South Asian (SAS) AF: 0.175 AC: 845 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2055 AN: 10568

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.192 AC: 13001 AN: 67856

Other (OTH) AF: 0.199 AC: 419 AN: 2104

Alfa AF: 0.199 Hom.: 360

Bravo AF: 0.194

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	16
DANN	Benign	0.93
PhyloP100		0.021
PromoterAI		0.012	Neutral
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

Other links and lift over

dbSNP: rs62234703; hg19: chr3-31574258;