chr22-35382285-A-G

Position:

• chr22-35382285-A-G

Variant summary

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

The NM_002133.3(HMOX1):​c.24-821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,034 control chromosomes in the GnomAD database, including 4,183 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 0.16 (4183 hom., cov: 32)
• Consequence: HMOX1 NM_002133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HMOX1	NM_002133.3	c.24-821A>G		intron_variant		ENST00000216117.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HMOX1	ENST00000216117.9	c.24-821A>G		intron_variant		1	NM_002133.3	P1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24339 AN: 151916 Hom.: 4174 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.160 AC: 24393 AN: 152034 Hom.: 4183 Cov.: 32 AF XY: 0.155 AC XY: 11493 AN XY: 74328

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0998 Hom.: 638

Bravo AF: 0.178

Asia WGS AF: 0.102 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.74

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: rs9306300; hg19: chr22-35778278;