dbSNP rs1051308: HMOX2:c.*544G>A (chr16-4510300-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002134.4(HMOX2):c.*544G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 159,512 control chromosomes in the GnomAD database, including 27,231 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 0.54 ( 25777 hom., cov: 32)

Exomes 𝑓: 0.62 ( 1454 hom. )

Consequence

HMOX2
NM_002134.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0570

Publications

38 publications found

Variant links:

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]

HMOX2 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HMOX2	NM_002134.4 link	c.*544G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000570646.6	NP_002125.3	P30519-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HMOX2	ENST00000570646.6 link	c.*544G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_002134.4	ENSP00000459214.1		P30519-1

Frequencies

GnomAD3 genomes

AF:

0.545

AC:

82835

AN:

151922

Hom.:

25768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.551

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.729

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.695

Gnomad OTH

AF:

0.573

GnomAD4 exome

AF:

0.618

AC:

4617

AN:

7472

Hom.:

1454

Cov.:

AF XY:

0.618

AC XY:

2456

AN XY:

3976

show subpopulations

African (AFR)

AF:

0.256

AC:

AN:

168

American (AMR)

AF:

0.504

AC:

363

AN:

720

Ashkenazi Jewish (ASJ)

AF:

0.687

AC:

114

AN:

166

East Asian (EAS)

AF:

0.631

AC:

279

AN:

442

South Asian (SAS)

AF:

0.484

AC:

152

AN:

314

European-Finnish (FIN)

AF:

0.661

AC:

271

AN:

410

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.652

AC:

3198

AN:

4906

Other (OTH)

AF:

0.571

AC:

193

AN:

338

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

184

275

367

459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.545

AC:

82861

AN:

152040

Hom.:

25777

Cov.:

AF XY:

0.545

AC XY:

40519

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.231

AC:

9588

AN:

41456

American (AMR)

AF:

0.552

AC:

8427

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.633

AC:

2198

AN:

3470

East Asian (EAS)

AF:

0.646

AC:

3339

AN:

5168

South Asian (SAS)

AF:

0.540

AC:

2604

AN:

4824

European-Finnish (FIN)

AF:

0.729

AC:

7706

AN:

10574

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.695

AC:

47229

AN:

67968

Other (OTH)

AF:

0.568

AC:

1198

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1638

3276

4914

6552

8190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.602

Hom.:

47030

Bravo

AF:

0.520

Asia WGS

AF:

0.494

AC:

1719

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

(source)

DANN

Benign

0.56

PhyloP100

0.057

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1051308

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over