rs4968596

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2

The NM_001003787.4(STRADA):c.36+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,612,884 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0045 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 57 hom. )

Consequence

STRADA
NM_001003787.4 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.167

Variant links:

Genes affected

STRADA (HGNC:30172): (STE20 related adaptor alpha) The protein encoded by this gene contains a STE20-like kinase domain, but lacks several residues that are critical for catalytic activity, so it is termed a 'pseudokinase'. The protein forms a heterotrimeric complex with serine/threonine kinase 11 (STK11, also known as LKB1) and the scaffolding protein calcium binding protein 39 (CAB39, also known as MO25). The protein activates STK11 leading to the phosphorylation of both proteins and excluding STK11 from the nucleus. The protein is necessary for STK11-induced G1 cell cycle arrest. A mutation in this gene has been shown to result in polyhydramnios, megalencephaly, and symptomatic epilepsy (PMSE) syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. Additional transcript variants have been described but their full-length nature is not known. [provided by RefSeq, Sep 2009]

STRADA 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=-0.32).

BP6

Variant 17-63728319-T-C is Benign according to our data. Variant chr17-63728319-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 377300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00452 (688/152180) while in subpopulation AMR AF= 0.0147 (225/15272). AF 95% confidence interval is 0.0132. There are 8 homozygotes in gnomad4. There are 464 alleles in male gnomad4 subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRADA	NM_001003787.4 linkuse as main transcript	c.36+15A>G		intron_variant		ENST00000336174.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRADA	ENST00000336174.12 linkuse as main transcript	c.36+15A>G		intron_variant		1	NM_001003787.4	P1	Q7RTN6-1

Frequencies

GnomAD3 genomes

AF:

0.00452

AC:

687

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000435

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0148

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.0117

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.0327

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000412

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00812

AC:

2033

AN:

250284

Hom.:

AF XY:

0.00674

AC XY:

912

AN XY:

135356

show subpopulations

Gnomad AFR exome

AF:

0.000310

Gnomad AMR exome

AF:

0.0318

Gnomad ASJ exome

AF:

0.000993

Gnomad EAS exome

AF:

0.00993

Gnomad SAS exome

AF:

0.000426

Gnomad FIN exome

AF:

0.0309

Gnomad NFE exome

AF:

0.000353

Gnomad OTH exome

AF:

0.00524

GnomAD4 exome

AF:

0.00253

AC:

3692

AN:

1460704

Hom.:

Cov.:

AF XY:

0.00230

AC XY:

1674

AN XY:

726708

show subpopulations

Gnomad4 AFR exome

AF:

0.000389

Gnomad4 AMR exome

AF:

0.0291

Gnomad4 ASJ exome

AF:

0.000842

Gnomad4 EAS exome

AF:

0.0174

Gnomad4 SAS exome

AF:

0.000499

Gnomad4 FIN exome

AF:

0.0267

Gnomad4 NFE exome

AF:

0.000109

Gnomad4 OTH exome

AF:

0.00149

GnomAD4 genome

AF:

0.00452

AC:

688

AN:

152180

Hom.:

Cov.:

AF XY:

0.00624

AC XY:

464

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.000433

Gnomad4 AMR

AF:

0.0147

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.0120

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.0327

Gnomad4 NFE

AF:

0.000412

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00146

Hom.:

Bravo

AF:

0.00389

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Feb 16, 2017

- -

Polyhydramnios, megalencephaly, and symptomatic epilepsy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

Cadd

Benign

Dann

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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