Genetic Variant STAU2:c.1531-554A>G (chr8-73423256-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001164380.2(STAU2):c.1531-554A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,030 control chromosomes in the GnomAD database, including 17,117 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 0.47 ( 17117 hom., cov: 32)

Consequence

STAU2
NM_001164380.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.603

Publications

2 publications found

Variant links:

Genes affected

STAU2 (HGNC:11371): (staufen double-stranded RNA binding protein 2) Staufen homolog 2 is a member of the family of double-stranded RNA (dsRNA)-binding proteins involved in the transport and/or localization of mRNAs to different subcellular compartments and/or organelles. These proteins are characterized by the presence of multiple dsRNA-binding domains which are required to bind RNAs having double-stranded secondary structures. Staufen homolog 2 shares 48.5% and 59.9% similarity with drosophila and human staufen, respectively. The exact function of Staufen homolog 2 is not known, but since it contains 3 copies of conserved dsRNA binding domain, it could be involved in double-stranded RNA binding events. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

STAU2 links:

STAU2-AS1 (HGNC:44101): (STAU2 antisense RNA 1)

STAU2-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164380.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STAU2	NM_001164380.2	MANE Select	c.1531-554A>G	intron	N/A	NP_001157852.1	Q9NUL3-1
STAU2	NM_001164381.2		c.1435-554A>G	intron	N/A	NP_001157853.1	Q9NUL3-2
STAU2	NM_001164382.2		c.1333-554A>G	intron	N/A	NP_001157854.1	Q9NUL3-7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STAU2	ENST00000524300.6	TSL:2 MANE Select	c.1531-554A>G	intron	N/A	ENSP00000428756.1	Q9NUL3-1
STAU2	ENST00000522695.5	TSL:1	c.1435-554A>G	intron	N/A	ENSP00000428456.1	Q9NUL3-2
STAU2	ENST00000946925.1		c.1537-554A>G	intron	N/A	ENSP00000616984.1

Frequencies

GnomAD3 genomes

AF:

0.468

AC:

71107

AN:

151912

Hom.:

17089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.453

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.468

AC:

71184

AN:

152030

Hom.:

17117

Cov.:

AF XY:

0.467

AC XY:

34681

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.557

AC:

23101

AN:

41486

American (AMR)

AF:

0.554

AC:

8469

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.401

AC:

1389

AN:

3468

East Asian (EAS)

AF:

0.286

AC:

1472

AN:

5138

South Asian (SAS)

AF:

0.286

AC:

1378

AN:

4818

European-Finnish (FIN)

AF:

0.421

AC:

4440

AN:

10556

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.437

AC:

29673

AN:

67958

Other (OTH)

AF:

0.451

AC:

955

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1968

3936

5903

7871

9839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.446

Hom.:

64912

Bravo

AF:

0.484

Asia WGS

AF:

0.328

AC:

1142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.54

PhyloP100

0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over