rs10982156

chr9-114325784-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000607.4(ORM1):c.541-508T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 151,362 control chromosomes in the GnomAD database, including 27 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 0.070 (27 hom., cov: 33)
• Consequence: ORM1 NM_000607.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

ORM1 (HGNC:8498): (orosomucoid 1) This gene encodes a key acute phase plasma protein. Because of its increase due to acute inflammation, this protein is classified as an acute-phase reactant. The specific function of this protein has not yet been determined; however, it may be involved in aspects of immunosuppression. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ORM1	NM_000607.4	c.541-508T>A		intron_variant		ENST00000259396.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ORM1	ENST00000259396.9	c.541-508T>A		intron_variant		1	NM_000607.4	P1

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10560 AN: 151242 Hom.: 27 Cov.: 33

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0697 AC: 10556 AN: 151362 Hom.: 27 Cov.: 33 AF XY: 0.0684 AC XY: 5067 AN XY: 74034

Gnomad4 AFR AF: 0.0756

Gnomad4 AMR AF: 0.0823

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.0688

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0706 Hom.: 0

Asia WGS AF: 0.0500 AC: 172 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.87
Dann	Benign	0.47

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: rs10982156; hg19: chr9-117088064;