8-73481391-A-G

Variant summary

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

The NM_001164380.2(STAU2):​c.1531-58689T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,628 control chromosomes in the GnomAD database, including 44,153 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 0.76 ( 44153 hom., cov: 29)

Consequence

STAU2
NM_001164380.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.634
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
STAU2NM_001164380.2 linkc.1531-58689T>C intron_variant ENST00000524300.6 NP_001157852.1 Q9NUL3-1
STAU2NM_001164381.2 linkc.1435-58689T>C intron_variant NP_001157853.1 Q9NUL3-2
STAU2NM_001164382.2 linkc.1332+46300T>C intron_variant NP_001157854.1 Q9NUL3-7
STAU2NM_001164383.2 linkc.1015-58689T>C intron_variant NP_001157855.1 Q9NUL3-6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
STAU2ENST00000524300.6 linkc.1531-58689T>C intron_variant 2 NM_001164380.2 ENSP00000428756.1 Q9NUL3-1
STAU2ENST00000522695.5 linkc.1435-58689T>C intron_variant 1 ENSP00000428456.1 Q9NUL3-2
STAU2ENST00000521210.5 linkc.1332+46300T>C intron_variant 2 ENSP00000429173.1 Q9NUL3-7
STAU2ENST00000523558.5 linkc.1015-58689T>C intron_variant 2 ENSP00000428741.1 Q9NUL3-6

Frequencies

GnomAD3 genomes
AF:
0.759
AC:
115061
AN:
151510
Hom.:
44097
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.791
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.803
Gnomad ASJ
AF:
0.699
Gnomad EAS
AF:
0.946
Gnomad SAS
AF:
0.870
Gnomad FIN
AF:
0.806
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.707
Gnomad OTH
AF:
0.749
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.760
AC:
115175
AN:
151628
Hom.:
44153
Cov.:
29
AF XY:
0.768
AC XY:
56921
AN XY:
74082
show subpopulations
Gnomad4 AFR
AF:
0.791
Gnomad4 AMR
AF:
0.803
Gnomad4 ASJ
AF:
0.699
Gnomad4 EAS
AF:
0.946
Gnomad4 SAS
AF:
0.870
Gnomad4 FIN
AF:
0.806
Gnomad4 NFE
AF:
0.707
Gnomad4 OTH
AF:
0.754
Alfa
AF:
0.718
Hom.:
49197
Bravo
AF:
0.759
Asia WGS
AF:
0.887
AC:
3083
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.7
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs4738371; hg19: chr8-74393626; API