rs10798738

Variant names:

• chr1-180192298-A-G
• rs10798738
• NM_002826.5:c.1288+1718A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
QSOX1	NM_002826.5	c.1288+1718A>G		intron_variant	Intron 10 of 11	ENST00000367602.8	NP_002817.2
QSOX1	NM_001004128.3	c.1288+1718A>G		intron_variant	Intron 10 of 12		NP_001004128.1
QSOX1	XM_047426230.1	c.1288+1718A>G		intron_variant	Intron 10 of 12		XP_047282186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QSOX1	ENST00000367602.8	c.1288+1718A>G		intron_variant	Intron 10 of 11	1	NM_002826.5	ENSP00000356574.3
QSOX1	ENST00000367600.5	c.1288+1718A>G		intron_variant	Intron 10 of 12	1		ENSP00000356572.5

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

African (AFR) AF: 0.869 AC: 36095 AN: 41530

American (AMR) AF: 0.961 AC: 14706 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3367 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4297 AN: 5142

South Asian (SAS) AF: 0.914 AC: 4412 AN: 4828

European-Finnish (FIN) AF: 0.966 AC: 10269 AN: 10628

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65191 AN: 68028

Other (OTH) AF: 0.943 AC: 1993 AN: 2114

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
PhyloP100		-1.5
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: rs10798738; hg19: chr1-180161433;