Variant 3-31532766-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0210

Variant links:

Genes affected

STT3B (HGNC:):

STT3B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.31532766A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28814

AN:

151704

Hom.:

2880

Cov.:

show subpopulations

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.:

AF XY:

0.200

AC XY:

47312

AN XY:

237118

show subpopulations

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.:

AF XY:

0.190

AC XY:

14080

AN XY:

74200

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over