chr9-136229894-A-C

Variant names:

• chr9-136229894-A-C
• rs12338076
• NM_181701.4:c.329-3020T>G

Variant summary

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

The NM_181701.4(QSOX2):​c.329-3020T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,162 control chromosomes in the GnomAD database, including 20,499 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 0.48 (20499 hom., cov: 33)
• Consequence: QSOX2 NM_181701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 31 publications found

Genes affected

QSOX2 (HGNC:30249): (quiescin sulfhydryl oxidase 2) QSOX2 is a member of the sulfhydryl oxidase/quiescin-6 (Q6) family (QSOX1; MIM 603120) that regulates the sensitization of neuroblastoma cells for IFN-gamma (IFNG; MIM 147570)-induced cell death (Wittke et al., 2003 [PubMed 14633699]).[supplied by OMIM, Jun 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QSOX2	NM_181701.4	c.329-3020T>G		intron_variant	Intron 1 of 11	ENST00000358701.10	NP_859052.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QSOX2	ENST00000358701.10	c.329-3020T>G		intron_variant	Intron 1 of 11	2	NM_181701.4	ENSP00000351536.5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72704 AN: 152044 Hom.: 20463 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.478 AC: 72805 AN: 152162 Hom.: 20499 Cov.: 33 AF XY: 0.475 AC XY: 35340 AN XY: 74400

African (AFR) AF: 0.804 AC: 33364 AN: 41508

American (AMR) AF: 0.462 AC: 7062 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1635 AN: 5176

South Asian (SAS) AF: 0.328 AC: 1584 AN: 4826

European-Finnish (FIN) AF: 0.334 AC: 3538 AN: 10592

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23157 AN: 67986

Other (OTH) AF: 0.438 AC: 926 AN: 2112

Alfa AF: 0.371 Hom.: 38614

Bravo AF: 0.502

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.033
DANN	Benign	0.28
PhyloP100		-1.7
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: rs12338076; hg19: chr9-139121740;