Variant rs11156654 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001083893.2(STRN3):c.282+11155A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 441,822 control chromosomes in the GnomAD database, including 13,059 homozygotes. 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: 𝑓 0.25 ( 5002 hom., cov: 29)

Exomes 𝑓: 0.22 ( 8057 hom. )

Consequence

STRN3
NM_001083893.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

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:

MIR624 (HGNC:32880): (microRNA 624) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR624 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRN3	NM_001083893.2 link	c.282+11155A>T		intron_variant		ENST00000357479.10	NP_001077362.1	Q13033-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
STRN3	ENST00000357479.10 link	c.282+11155A>T	intron_variant	5	NM_001083893.2	ENSP00000350071.5	Q13033-1
STRN3	ENST00000355683.9 link	c.282+11155A>T	intron_variant	1		ENSP00000347909.5	Q13033-2
STRN3	ENST00000555358.5 link	n.282+11155A>T	intron_variant	1		ENSP00000451028.1	G3V340
MIR624	ENST00000385217.1 link	n.-7A>T	upstream_gene_variant	6

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37811

AN:

151436

Hom.:

5001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.235

GnomAD3 exomes

AF:

0.204

AC:

26296

AN:

129210

Hom.:

3086

AF XY:

0.201

AC XY:

13793

AN XY:

68558

show subpopulations

Gnomad AFR exome

AF:

0.292

Gnomad AMR exome

AF:

0.122

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.00140

Gnomad SAS exome

AF:

0.148

Gnomad FIN exome

AF:

0.262

Gnomad NFE exome

AF:

0.248

Gnomad OTH exome

AF:

0.219

GnomAD4 exome

AF:

0.222

AC:

64583

AN:

290270

Hom.:

8057

Cov.:

AF XY:

0.218

AC XY:

36073

AN XY:

165456

show subpopulations

Gnomad4 AFR exome

AF:

0.275

Gnomad4 AMR exome

AF:

0.116

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.00101

Gnomad4 SAS exome

AF:

0.157

Gnomad4 FIN exome

AF:

0.264

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.250

AC:

37826

AN:

151552

Hom.:

5002

Cov.:

AF XY:

0.246

AC XY:

18191

AN XY:

74040

show subpopulations

Gnomad4 AFR

AF:

0.301

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.245

Gnomad4 EAS

AF:

0.00271

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.232

Alfa

AF:

0.258

Hom.:

1690

Bravo

AF:

0.243

Asia WGS

AF:

0.0710

AC:

249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.3

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over