9-136220024-G-T

Position:

• chr9-136220024-G-T

Variant summary

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

The NM_181701.4(QSOX2):​c.822-860C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,004 control chromosomes in the GnomAD database, including 18,534 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 0.46 (18534 hom., cov: 32)
• Consequence: QSOX2 NM_181701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
QSOX2	NM_181701.4	c.822-860C>A		intron_variant		ENST00000358701.10	NP_859052.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QSOX2	ENST00000358701.10	c.822-860C>A		intron_variant		2	NM_181701.4	ENSP00000351536	P1
QSOX2	ENST00000455222.1	c.124-860C>A		intron_variant		5		ENSP00000389089

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69787 AN: 151886 Hom.: 18499 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.460 AC: 69884 AN: 152004 Hom.: 18534 Cov.: 32 AF XY: 0.456 AC XY: 33894 AN XY: 74272

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.418

Alfa AF: 0.360 Hom.: 6328

Bravo AF: 0.482

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.30

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: rs7849585; hg19: chr9-139111870;