rs55946907

Variant names:

• chr1-180161588-C-T
• rs55946907
• NM_002826.5:c.266-4903C>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.266-4903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,240 control chromosomes in the GnomAD database, including 317 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 (317 hom., cov: 32)
• Consequence: QSOX1 NM_002826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002826.5. 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
	QSOX1	NM_002826.5	MANE Select	c.266-4903C>T		intron	N/A	NP_002817.2
	QSOX1	NM_001004128.3		c.266-4903C>T		intron	N/A	NP_001004128.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QSOX1	ENST00000367602.8	TSL:1 MANE Select	c.266-4903C>T		intron	N/A	ENSP00000356574.3
	QSOX1	ENST00000367600.5	TSL:1	c.266-4903C>T		intron	N/A	ENSP00000356572.5
	QSOX1	ENST00000392029.6	TSL:5	n.266-4903C>T		intron	N/A	ENSP00000375883.2

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8026 AN: 152122 Hom.: 317 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0527 AC: 8022 AN: 152240 Hom.: 317 Cov.: 32 AF XY: 0.0510 AC XY: 3792 AN XY: 74424

African (AFR) AF: 0.0166 AC: 689 AN: 41542

American (AMR) AF: 0.0400 AC: 612 AN: 15302

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4818

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0826 AC: 5615 AN: 68000

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0469 Hom.: 99

Bravo AF: 0.0483

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		0.44
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: rs55946907; hg19: chr1-180130723;