rs10798738

Positions:

• chr1-180192298-A-G
• chr1-180192298-A-T

Variant summary

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

The NM_002826.5(QSOX1):​c.1288+1718A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,252 control chromosomes in the GnomAD database, including 65,820 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 0.93 (65820 hom., cov: 32)
• Consequence: QSOX1 NM_002826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

QSOX1 (HGNC:9756): (quiescin sulfhydryl oxidase 1) This gene encodes a protein that contains domains of thioredoxin and ERV1, members of two long-standing gene families. The gene expression is induced as fibroblasts begin to exit the proliferative cycle and enter quiescence, suggesting that this gene plays an important role in growth regulation. Two transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QSOX1	NM_002826.5	c.1288+1718A>G		intron_variant		ENST00000367602.8
QSOX1	NM_001004128.3	c.1288+1718A>G		intron_variant
QSOX1	XM_047426230.1	c.1288+1718A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QSOX1	ENST00000367602.8	c.1288+1718A>G		intron_variant		1	NM_002826.5	P2
QSOX1	ENST00000367600.5	c.1288+1718A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141289 AN: 152134 Hom.: 65779 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.929 AC: 141387 AN: 152252 Hom.: 65820 Cov.: 32 AF XY: 0.930 AC XY: 69200 AN XY: 74428

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.943

Alfa AF: 0.942 Hom.: 9840

Bravo AF: 0.923

Asia WGS AF: 0.888 AC: 3089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.16

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: rs10798738; hg19: chr1-180161433;