Variant 2-36867802-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003162.4(STRN):c.1547+12T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.974 in 1,532,196 control chromosomes in the GnomAD database, including 728,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.91 ( 64484 hom., cov: 32)

Exomes 𝑓: 0.98 ( 664321 hom. )

Consequence

STRN
NM_003162.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.16

Variant links:

Genes affected

STRN (HGNC:11424): (striatin) Enables armadillo repeat domain binding activity; estrogen receptor binding activity; and protein phosphatase 2A binding activity. Involved in Wnt signaling pathway and negative regulation of cell population proliferation. Located in bicellular tight junction. Part of FAR/SIN/STRIPAK complex. [provided by Alliance of Genome Resources, Apr 2022]

STRN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 2-36867802-A-G is Benign according to our data. Variant chr2-36867802-A-G is described in ClinVar as [Benign]. Clinvar id is 1239451.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
STRN	NM_003162.4 linkuse as main transcript	c.1547+12T>C	intron_variant	ENST00000263918.9
STRN	XM_005264519.6 linkuse as main transcript	c.1436+12T>C	intron_variant
STRN	XM_011533073.3 linkuse as main transcript	c.1634+12T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRN	ENST00000263918.9 linkuse as main transcript	c.1547+12T>C		intron_variant		1	NM_003162.4	P1	O43815-1

Frequencies

GnomAD3 genomes

AF:

0.914

AC:

138973

AN:

152070

Hom.:

64458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.940

Gnomad AMR

AF:

0.959

Gnomad ASJ

AF:

0.997

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.987

Gnomad FIN

AF:

0.978

Gnomad MID

AF:

0.965

Gnomad NFE

AF:

0.986

Gnomad OTH

AF:

0.937

GnomAD3 exomes

AF:

0.970

AC:

205343

AN:

211704

Hom.:

100022

AF XY:

0.975

AC XY:

112580

AN XY:

115498

show subpopulations

Gnomad AFR exome

AF:

0.735

Gnomad AMR exome

AF:

0.984

Gnomad ASJ exome

AF:

0.998

Gnomad EAS exome

AF:

0.999

Gnomad SAS exome

AF:

0.988

Gnomad FIN exome

AF:

0.979

Gnomad NFE exome

AF:

0.986

Gnomad OTH exome

AF:

0.981

GnomAD4 exome

AF:

0.980

AC:

1352889

AN:

1380008

Hom.:

664321

Cov.:

AF XY:

0.981

AC XY:

674768

AN XY:

687616

show subpopulations

Gnomad4 AFR exome

AF:

0.729

Gnomad4 AMR exome

AF:

0.980

Gnomad4 ASJ exome

AF:

0.997

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.989

Gnomad4 FIN exome

AF:

0.980

Gnomad4 NFE exome

AF:

0.986

Gnomad4 OTH exome

AF:

0.970

GnomAD4 genome

AF:

0.914

AC:

139046

AN:

152188

Hom.:

64484

Cov.:

AF XY:

0.916

AC XY:

68140

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.733

Gnomad4 AMR

AF:

0.959

Gnomad4 ASJ

AF:

0.997

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.987

Gnomad4 FIN

AF:

0.978

Gnomad4 NFE

AF:

0.986

Gnomad4 OTH

AF:

0.937

Alfa

AF:

0.972

Hom.:

69361

Bravo

AF:

0.903

Asia WGS

AF:

0.976

AC:

3380

AN:

3464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.51

DANN

Benign

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over