chr9-136220024-G-T

Variant names:

• chr9-136220024-G-T
• rs7849585
• NM_181701.4:c.822-860C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 49 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181701.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QSOX2	NM_181701.4	MANE Select	c.822-860C>A		intron	N/A	NP_859052.3	Q6ZRP7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QSOX2	ENST00000358701.10	TSL:2 MANE Select	c.822-860C>A		intron	N/A	ENSP00000351536.5	Q6ZRP7
	QSOX2	ENST00000455222.1	TSL:5	c.123-860C>A		intron	N/A	ENSP00000389089.1	H0Y430

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

African (AFR) AF: 0.753 AC: 31211 AN: 41470

American (AMR) AF: 0.446 AC: 6822 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3464

East Asian (EAS) AF: 0.316 AC: 1626 AN: 5152

South Asian (SAS) AF: 0.326 AC: 1567 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3495 AN: 10562

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22725 AN: 67932

Other (OTH) AF: 0.418 AC: 882 AN: 2112

Alfa AF: 0.364 Hom.: 23850

Bravo AF: 0.482

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.30
PhyloP100		-2.5
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: rs7849585; hg19: chr9-139111870;