1-180185365-C-T

Variant names:

• chr1-180185365-C-T
• rs17299701
• NM_002826.5:c.888-688C>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.888-688C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,294 control chromosomes in the GnomAD database, including 321 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 0.053 (321 hom., cov: 33)
• Consequence: QSOX1 NM_002826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QSOX1	NM_002826.5	c.888-688C>T		intron_variant	Intron 7 of 11	ENST00000367602.8	NP_002817.2
QSOX1	NM_001004128.3	c.888-688C>T		intron_variant	Intron 7 of 12		NP_001004128.1
QSOX1	XM_047426230.1	c.888-688C>T		intron_variant	Intron 7 of 12		XP_047282186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QSOX1	ENST00000367602.8	c.888-688C>T		intron_variant	Intron 7 of 11	1	NM_002826.5	ENSP00000356574.3
QSOX1	ENST00000367600.5	c.888-688C>T		intron_variant	Intron 7 of 12	1		ENSP00000356572.5
QSOX1	ENST00000392029.6	n.*317-688C>T		intron_variant	Intron 6 of 7	5		ENSP00000375883.2

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8055 AN: 152176 Hom.: 321 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0529 AC: 8051 AN: 152294 Hom.: 321 Cov.: 33 AF XY: 0.0511 AC XY: 3808 AN XY: 74464

African (AFR) AF: 0.0165 AC: 687 AN: 41568

American (AMR) AF: 0.0397 AC: 607 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00248 AC: 12 AN: 4830

European-Finnish (FIN) AF: 0.0813 AC: 863 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5640 AN: 68010

Other (OTH) AF: 0.0451 AC: 95 AN: 2108

Alfa AF: 0.0622 Hom.: 56

Bravo AF: 0.0483

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		0.40
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: rs17299701; hg19: chr1-180154500;