rs4738367

chr8-73480665-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164380.2(STAU2):c.1531-57963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,018 control chromosomes in the GnomAD database, including 32,288 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 0.65 (32288 hom., cov: 33)
• Consequence: STAU2 NM_001164380.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAU2	NM_001164380.2	c.1531-57963C>T		intron_variant		ENST00000524300.6
STAU2	NM_001164381.2	c.1435-57963C>T		intron_variant
STAU2	NM_001164382.2	c.1332+47026C>T		intron_variant
STAU2	NM_001164383.2	c.1015-57963C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAU2	ENST00000524300.6	c.1531-57963C>T		intron_variant		2	NM_001164380.2	P1
STAU2	ENST00000522695.5	c.1435-57963C>T		intron_variant		1
STAU2	ENST00000521210.5	c.1332+47026C>T		intron_variant		2
STAU2	ENST00000523558.5	c.1015-57963C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98163 AN: 151900 Hom.: 32246 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.646 AC: 98260 AN: 152018 Hom.: 32288 Cov.: 33 AF XY: 0.657 AC XY: 48768 AN XY: 74282

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.662

Alfa AF: 0.646 Hom.: 43346

Bravo AF: 0.646

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.53

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

Other links and lift over

dbSNP: rs4738367; hg19: chr8-74392900;