rs4738367

Variant names:

• chr8-73480665-G-A
• rs4738367
• NM_001164380.2:c.1531-57963C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STAU2	NM_001164380.2	c.1531-57963C>T		intron_variant	Intron 13 of 14	ENST00000524300.6	NP_001157852.1
STAU2	NM_001164381.2	c.1435-57963C>T		intron_variant	Intron 12 of 13		NP_001157853.1
STAU2	NM_001164382.2	c.1332+47026C>T		intron_variant	Intron 12 of 13		NP_001157854.1
STAU2	NM_001164383.2	c.1015-57963C>T		intron_variant	Intron 8 of 9		NP_001157855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAU2	ENST00000524300.6	c.1531-57963C>T		intron_variant	Intron 13 of 14	2	NM_001164380.2	ENSP00000428756.1
STAU2	ENST00000522695.5	c.1435-57963C>T		intron_variant	Intron 10 of 11	1		ENSP00000428456.1
STAU2	ENST00000521210.5	c.1332+47026C>T		intron_variant	Intron 12 of 13	2		ENSP00000429173.1
STAU2	ENST00000523558.5	c.1015-57963C>T		intron_variant	Intron 8 of 9	2		ENSP00000428741.1

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

African (AFR) AF: 0.562 AC: 23324 AN: 41468

American (AMR) AF: 0.736 AC: 11233 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2275 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4686 AN: 5146

South Asian (SAS) AF: 0.742 AC: 3574 AN: 4816

European-Finnish (FIN) AF: 0.733 AC: 7760 AN: 10582

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43329 AN: 67952

Other (OTH) AF: 0.662 AC: 1398 AN: 2112

Alfa AF: 0.646 Hom.: 54716

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
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4738367; hg19: chr8-74392900;