3-31532901-T-TTCCTCC

Position:

• chr3-31532901-T-TTCCTCC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000453168.5(STT3B):​n.264_265insTCCTCC 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 0.0478 in 1,395,718 control chromosomes in the GnomAD database, including 1,871 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.042 (337 hom., cov: 32)
  • Exomes 𝑓: 0.049 (1534 hom.)
• Consequence: STT3B ENST00000453168.5 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.833

Genes affected

STT3B (HGNC:):

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 -10 ACMG points.

• BP6: Variant 3-31532901-T-TTCCTCC is Benign according to our data. Variant chr3-31532901-T-TTCCTCC is described in ClinVar as [Benign]. Clinvar id is 1245369.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31532901_31532902insTCCTCC		intergenic_region
STT3B	NM_178862.3	c.-98_-97insTCCTCC		upstream_gene_variant		ENST00000295770.4	NP_849193.1
STT3B	XM_011533465.2	c.-98_-97insTCCTCC		upstream_gene_variant			XP_011531767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3B	ENST00000453168.5	n.264_265insTCCTCC		non_coding_transcript_exon_variant	1/10	1
STT3B	ENST00000295770.4	c.-98_-97insTCCTCC		upstream_gene_variant		1	NM_178862.3	ENSP00000295770.2

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6417 AN: 151192 Hom.: 339 Cov.: 32

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.0277

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0552

GnomAD4 exome AF: 0.0485 AC: 60371 AN: 1244418 Hom.: 1534 Cov.: 31 AF XY: 0.0481 AC XY: 29270 AN XY: 608750

Gnomad4 AFR exome AF: 0.00655

Gnomad4 AMR exome AF: 0.0216

Gnomad4 ASJ exome AF: 0.0460

Gnomad4 EAS exome AF: 0.273

Gnomad4 SAS exome AF: 0.0408

Gnomad4 FIN exome AF: 0.0431

Gnomad4 NFE exome AF: 0.0439

Gnomad4 OTH exome AF: 0.0600

GnomAD4 genome AF: 0.0424 AC: 6414 AN: 151300 Hom.: 337 Cov.: 32 AF XY: 0.0440 AC XY: 3251 AN XY: 73928

Gnomad4 AFR AF: 0.00956

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0417

Gnomad4 OTH AF: 0.0575

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

May 24, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs529181821; hg19: chr3-31574393;