1-180185365-C-T

Position:

• chr1-180185365-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• 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/exons	MANE	Protein	UniProt
QSOX1	NM_002826.5	c.888-688C>T		intron_variant		ENST00000367602.8	NP_002817.2
QSOX1	NM_001004128.3	c.888-688C>T		intron_variant			NP_001004128.1
QSOX1	XM_047426230.1	c.888-688C>T		intron_variant			XP_047282186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QSOX1	ENST00000367602.8	c.888-688C>T		intron_variant		1	NM_002826.5	ENSP00000356574.3
QSOX1	ENST00000367600.5	c.888-688C>T		intron_variant		1		ENSP00000356572.5
QSOX1	ENST00000392029.6	n.*317-688C>T		intron_variant		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

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00248

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.0829

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0643 Hom.: 55

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

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: rs17299701; hg19: chr1-180154500;