Variant 14-30919106-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001083893.2(STRN3):c.1100G>A(p.Arg367Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00136 in 1,599,624 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 8 hom. )

Consequence

STRN3
NM_001083893.2 missense, splice_region

Scores

Splicing: ADA: 0.9995

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.67

Variant links:

Genes affected

STRN3 (HGNC:15720): (striatin 3) Enables armadillo repeat domain binding activity; protein phosphatase 2A binding activity; and small GTPase binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in Golgi apparatus; nucleoplasm; and plasma membrane. Part of FAR/SIN/STRIPAK complex. [provided by Alliance of Genome Resources, Apr 2022]

STRN3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 14-30919106-C-T is Benign according to our data. Variant chr14-30919106-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644151.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd at 389 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRN3	NM_001083893.2 linkuse as main transcript	c.1100G>A	p.Arg367Lys	missense_variant, splice_region_variant	9/18	ENST00000357479.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN3	ENST00000357479.10 linkuse as main transcript	c.1100G>A	p.Arg367Lys	missense_variant, splice_region_variant	9/18	5	NM_001083893.2	P3	Q13033-1

Frequencies

GnomAD3 genomes

AF:

0.00256

AC:

389

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00432

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.0188

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00193

AC:

465

AN:

241006

Hom.:

AF XY:

0.00182

AC XY:

239

AN XY:

131020

show subpopulations

Gnomad AFR exome

AF:

0.00398

Gnomad AMR exome

AF:

0.00279

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000680

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00117

Gnomad OTH exome

AF:

0.00330

GnomAD4 exome

AF:

0.00124

AC:

1788

AN:

1447418

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

892

AN XY:

720272

show subpopulations

Gnomad4 AFR exome

AF:

0.00503

Gnomad4 AMR exome

AF:

0.00273

Gnomad4 ASJ exome

AF:

0.0181

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000119

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000741

Gnomad4 OTH exome

AF:

0.00309

GnomAD4 genome

AF:

0.00256

AC:

390

AN:

152206

Hom.:

Cov.:

AF XY:

0.00253

AC XY:

188

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00431

Gnomad4 AMR

AF:

0.00373

Gnomad4 ASJ

AF:

0.0188

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00109

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00284

Hom.:

Bravo

AF:

0.00293

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.00285

AC:

ESP6500EA

AF:

0.00194

AC:

ExAC

AF:

0.00157

AC:

190

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

STRN3: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.36

Cadd

Uncertain

Dann

Uncertain

0.99

DEOGEN2

Benign

0.0028

Eigen

Uncertain

0.36

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.48

M_CAP

Benign

0.059

MetaRNN

Benign

0.0076

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

D;D

PROVEAN

Benign

1.7

REVEL

Uncertain

0.29

Sift

Benign

1.0

Sift4G

Benign

1.0

MVP

0.69

ClinPred

0.060

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.92

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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