NM_001164380.2:c.1531-58689T>C

Variant names:

• chr8-73481391-A-G
• rs4738371
• NM_001164380.2:c.1531-58689T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164380.2(STAU2):​c.1531-58689T>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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 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=-0.95).
• 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 rank	MANE	Protein	UniProt
STAU2	NM_001164380.2	c.1531-58689T>C		intron_variant	Intron 13 of 14	ENST00000524300.6	NP_001157852.1
STAU2	NM_001164381.2	c.1435-58689T>C		intron_variant	Intron 12 of 13		NP_001157853.1
STAU2	NM_001164382.2	c.1332+46300T>C		intron_variant	Intron 12 of 13		NP_001157854.1
STAU2	NM_001164383.2	c.1015-58689T>C		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.1531-58689T>C		intron_variant	Intron 13 of 14	2	NM_001164380.2	ENSP00000428756.1
STAU2	ENST00000522695.5	c.1435-58689T>C		intron_variant	Intron 10 of 11	1		ENSP00000428456.1
STAU2	ENST00000521210.5	c.1332+46300T>C		intron_variant	Intron 12 of 13	2		ENSP00000429173.1
STAU2	ENST00000523558.5	c.1015-58689T>C		intron_variant	Intron 8 of 9	2		ENSP00000428741.1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115061 AN: 151510 Hom.: 44097 Cov.: 29

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

African (AFR) AF: 0.791 AC: 32685 AN: 41320

American (AMR) AF: 0.803 AC: 12236 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2422 AN: 3466

East Asian (EAS) AF: 0.946 AC: 4847 AN: 5124

South Asian (SAS) AF: 0.870 AC: 4166 AN: 4790

European-Finnish (FIN) AF: 0.806 AC: 8481 AN: 10518

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48017 AN: 67870

Other (OTH) AF: 0.754 AC: 1584 AN: 2102

Alfa AF: 0.723 Hom.: 62334

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
PhyloP100		-0.63
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: rs4738371; hg19: chr8-74393626;