chr1-180161588-C-T

Position:

• chr1-180161588-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.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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
QSOX1	NM_002826.5	c.266-4903C>T		intron_variant		ENST00000367602.8	NP_002817.2
QSOX1	NM_001004128.3	c.266-4903C>T		intron_variant			NP_001004128.1
QSOX1	XM_047426230.1	c.266-4903C>T		intron_variant			XP_047282186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QSOX1	ENST00000367602.8	c.266-4903C>T		intron_variant		1	NM_002826.5	ENSP00000356574	P2
QSOX1	ENST00000367600.5	c.266-4903C>T		intron_variant		1		ENSP00000356572	A2
QSOX1	ENST00000392029.6	c.266-4903C>T		intron_variant, NMD_transcript_variant		5		ENSP00000375883

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

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0638 Hom.: 53

Bravo AF: 0.0483

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.63

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: rs55946907; hg19: chr1-180130723;