rs4737384

chr8-73483605-A-Gchr8-73483605-A-T

Variant summary

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

The NM_001164380.2(STAU2):c.1531-60903T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,958 control chromosomes in the GnomAD database, including 20,289 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 0.51 (20289 hom., cov: 33)
• Consequence: STAU2 NM_001164380.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.45

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=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAU2	NM_001164380.2	c.1531-60903T>C		intron_variant		ENST00000524300.6
STAU2	NM_001164381.2	c.1435-60903T>C		intron_variant
STAU2	NM_001164382.2	c.1332+44086T>C		intron_variant
STAU2	NM_001164383.2	c.1015-60903T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAU2	ENST00000524300.6	c.1531-60903T>C		intron_variant		2	NM_001164380.2	P1
STAU2	ENST00000522695.5	c.1435-60903T>C		intron_variant		1
STAU2	ENST00000521210.5	c.1332+44086T>C		intron_variant		2
STAU2	ENST00000523558.5	c.1015-60903T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77849 AN: 151840 Hom.: 20257 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.513 AC: 77927 AN: 151958 Hom.: 20289 Cov.: 33 AF XY: 0.516 AC XY: 38312 AN XY: 74272

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.507

Alfa AF: 0.544 Hom.: 3855

Bravo AF: 0.521

Asia WGS AF: 0.454 AC: 1581 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	17
Dann	Benign	0.78

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: rs4737384; hg19: chr8-74395840;