rs9622194

Variant summary

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

The NM_002133.3(HMOX1):​c.736+1007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,188 control chromosomes in the GnomAD database, including 3,429 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 0.12 ( 3429 hom., cov: 31)

Consequence

HMOX1
NM_002133.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Publications

2 publications found
Variant links:
Genes affected
HMOX1 (HGNC:5013): (heme oxygenase 1) 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. [provided by RefSeq, Jul 2008]
HMOX1 Gene-Disease associations (from GenCC):
  • heme oxygenase 1 deficiency
    Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet
  • cystic fibrosis
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • chronic obstructive pulmonary disease
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HMOX1NM_002133.3 linkc.736+1007G>A intron_variant Intron 4 of 4 ENST00000216117.9 NP_002124.1 P09601Q6FH11

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HMOX1ENST00000216117.9 linkc.736+1007G>A intron_variant Intron 4 of 4 1 NM_002133.3 ENSP00000216117.8 P09601

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18116
AN:
152070
Hom.:
3421
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.399
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0448
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.0407
Gnomad SAS
AF:
0.0805
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00238
Gnomad OTH
AF:
0.0788
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.119
AC:
18168
AN:
152188
Hom.:
3429
Cov.:
31
AF XY:
0.117
AC XY:
8696
AN XY:
74404
show subpopulations
African (AFR)
AF:
0.399
AC:
16528
AN:
41454
American (AMR)
AF:
0.0448
AC:
685
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.00432
AC:
15
AN:
3472
East Asian (EAS)
AF:
0.0406
AC:
210
AN:
5170
South Asian (SAS)
AF:
0.0810
AC:
391
AN:
4830
European-Finnish (FIN)
AF:
0.000188
AC:
2
AN:
10620
Middle Eastern (MID)
AF:
0.0306
AC:
9
AN:
294
European-Non Finnish (NFE)
AF:
0.00238
AC:
162
AN:
68024
Other (OTH)
AF:
0.0784
AC:
166
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
568
1137
1705
2274
2842
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
162
324
486
648
810
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0287
Hom.:
73
Bravo
AF:
0.134
Asia WGS
AF:
0.0770
AC:
267
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
4.3
DANN
Benign
0.30
PhyloP100
-0.18
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs9622194; hg19: chr22-35786963; API