chr16-4490884-A-G

Variant names:

• chr16-4490884-A-G
• rs9929475
• NM_002134.4:c.-42+14397A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002134.4(HMOX2):​c.-42+14397A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,024 control chromosomes in the GnomAD database, including 26,749 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 0.57 (26749 hom., cov: 32)
• Consequence: HMOX2 NM_002134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 15 publications found

Genes affected

HMOX2 (HGNC:5014): (heme oxygenase 2) Heme oxygenase, an essential enzyme in heme catabolism, cleaves heme to form biliverdin, which is subsequently converted to bilirubin by biliverdin reductase, and carbon monoxide, a putative neurotransmitter. Heme oxygenase activity is induced by its substrate heme and by various nonheme substances. Heme oxygenase occurs as 2 isozymes, an inducible heme oxygenase-1 and a constitutive heme oxygenase-2. HMOX1 and HMOX2 belong to the heme oxygenase family. Several alternatively spliced transcript variants encoding three different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

NMRAL1 (HGNC:24987): (NmrA like redox sensor 1) This gene encodes an NADPH sensor protein that preferentially binds to NADPH. The encoded protein also negatively regulates the activity of NF-kappaB in a ubiquitylation-dependent manner. It plays a key role in cellular antiviral response by negatively regulating the interferon response factor 3-mediated expression of interferon beta. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]

LOC124903636 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMOX2	NM_002134.4	MANE Select	c.-42+14397A>G		intron	N/A	NP_002125.3
	HMOX2	NM_001286267.2		c.1-5262A>G		intron	N/A	NP_001273196.1
	HMOX2	NM_001127204.2		c.-42+7130A>G		intron	N/A	NP_001120676.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMOX2	ENST00000570646.6	TSL:1 MANE Select	c.-42+14397A>G		intron	N/A	ENSP00000459214.1
	HMOX2	ENST00000219700.10	TSL:5	c.-42+14467A>G		intron	N/A	ENSP00000219700.6
	HMOX2	ENST00000406590.6	TSL:5	c.-41-14600A>G		intron	N/A	ENSP00000385100.2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85974 AN: 151908 Hom.: 26735 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.566 AC: 86022 AN: 152024 Hom.: 26749 Cov.: 32 AF XY: 0.565 AC XY: 41979 AN XY: 74304

African (AFR) AF: 0.295 AC: 12243 AN: 41434

American (AMR) AF: 0.563 AC: 8597 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2181 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3373 AN: 5164

South Asian (SAS) AF: 0.544 AC: 2619 AN: 4818

European-Finnish (FIN) AF: 0.731 AC: 7724 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47484 AN: 67978

Other (OTH) AF: 0.584 AC: 1232 AN: 2110

Alfa AF: 0.580 Hom.: 4190

Bravo AF: 0.544

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		0.64
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: rs9929475; hg19: chr16-4540885;