ENST00000453168.5:n.10C>G

Variant names:

• chr3-31532647-C-G
• rs529595925
• ENST00000453168.5:n.10C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000453168.5(STT3B):​n.10C>G 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 0.0000113 in 265,226 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: STT3B ENST00000453168.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453168.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STT3B	ENST00000453168.5	TSL:1	n.10C>G		non_coding_transcript_exon	Exon 1 of 10
	STT3B	ENST00000935233.1		c.-352C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	ENSP00000605292.1
	STT3B	ENST00000868023.1		c.-352C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000538082.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000113 AC: 3 AN: 265226 Hom.: 0 Cov.: 0 AF XY: 0.00000733 AC XY: 1 AN XY: 136474

African (AFR) AF: 0.00 AC: 0 AN: 7236

American (AMR) AF: 0.00 AC: 0 AN: 7600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9512

East Asian (EAS) AF: 0.00 AC: 0 AN: 22920

South Asian (SAS) AF: 0.00 AC: 0 AN: 8636

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21868

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1352

European-Non Finnish (NFE) AF: 0.0000178 AC: 3 AN: 169012

Other (OTH) AF: 0.00 AC: 0 AN: 17090

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		-0.091
PromoterAI		-0.018	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: rs529595925; hg19: chr3-31574139;