Genetic Variant STT3B:n.280_285dupTCCTCC (chr3-31532901-T-TTCCTCC) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000935233.1(STT3B):c.-82_-77dupTCCTCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 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
ENST00000935233.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.833

Publications

1 publications found

Variant links:

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)

STT3B links:

ENSG00000288926 (HGNC:):

ENSG00000288926 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

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.-98_-97insTCCTCC		upstream_gene	N/A	NP_849193.1	Q8TCJ2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STT3B	ENST00000453168.5	TSL:1	n.280_285dupTCCTCC	non_coding_transcript_exon	Exon 1 of 10
STT3B	ENST00000935233.1		c.-82_-77dupTCCTCC	5_prime_UTR	Exon 1 of 16	ENSP00000605292.1
STT3B	ENST00000868023.1		c.-82_-77dupTCCTCC	5_prime_UTR	Exon 1 of 15	ENSP00000538082.1

Frequencies

GnomAD3 genomes

AF:

0.0424

AC:

6417

AN:

151192

Hom.:

339

Cov.:

show subpopulations

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.:

AF XY:

0.0481

AC XY:

29270

AN XY:

608750

show subpopulations

African (AFR)

AF:

0.00655

AC:

162

AN:

24720

American (AMR)

AF:

0.0216

AC:

303

AN:

13996

Ashkenazi Jewish (ASJ)

AF:

0.0460

AC:

813

AN:

17666

East Asian (EAS)

AF:

0.273

AC:

7567

AN:

27716

South Asian (SAS)

AF:

0.0408

AC:

2400

AN:

58774

European-Finnish (FIN)

AF:

0.0431

AC:

1792

AN:

41552

Middle Eastern (MID)

AF:

0.0339

AC:

153

AN:

4510

European-Non Finnish (NFE)

AF:

0.0439

AC:

44162

AN:

1005194

Other (OTH)

AF:

0.0600

AC:

3019

AN:

50290

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

2603

5206

7810

10413

13016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1926

3852

5778

7704

9630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0424

AC:

6414

AN:

151300

Hom.:

337

Cov.:

AF XY:

0.0440

AC XY:

3251

AN XY:

73928

show subpopulations

African (AFR)

AF:

0.00956

AC:

396

AN:

41414

American (AMR)

AF:

0.0373

AC:

568

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.0479

AC:

166

AN:

3466

East Asian (EAS)

AF:

0.304

AC:

1497

AN:

4922

South Asian (SAS)

AF:

0.0520

AC:

249

AN:

4792

European-Finnish (FIN)

AF:

0.0533

AC:

556

AN:

10434

Middle Eastern (MID)

AF:

0.0377

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0417

AC:

2825

AN:

67740

Other (OTH)

AF:

0.0575

AC:

121

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

274

549

823

1098

1372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00568

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.83

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over