chr1-151769857-G-A

Position:

• chr1-151769857-G-A

Variant summary

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

The NM_016178.2(OAZ3):​c.480-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,238 control chromosomes in the GnomAD database, including 1,893 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 0.15 (1893 hom., cov: 32)
• Consequence: OAZ3 NM_016178.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

OAZ3 (HGNC:8097): (ornithine decarboxylase antizyme 3) The protein encoded by this gene belongs to the ornithine decarboxylase antizyme family, which plays a role in cell growth and proliferation by regulating intracellular polyamine levels. Expression of antizymes requires +1 ribosomal frameshifting, which is enhanced by high levels of polyamines. Antizymes in turn bind to and inhibit ornithine decarboxylase (ODC), the key enzyme in polyamine biosynthesis; thus, completing the auto-regulatory circuit. This gene encodes antizyme 3, the third member of the antizyme family. Like antizymes 1 and 2, antizyme 3 inhibits ODC activity and polyamine uptake; however, it does not stimulate ODC degradation. Also, while antizymes 1 and 2 have broad tissue distribution, expression of antizyme 3 is restricted to haploid germ cells in testis, suggesting a distinct role for this antizyme in spermiogenesis. Antizyme 3 gene knockout studies showed that homozygous mutant male mice were infertile, and indicated the likely role of this antizyme in the formation of a rigid connection between the sperm head and tail during spermatogenesis. Alternatively spliced transcript variants encoding different isoforms, including one resulting from the use of non-AUG (CUG) translation initiation codon, have been found for this gene. [provided by RefSeq, Dec 2014]

TDRKH (HGNC:11713): (tudor and KH domain containing) Predicted to enable RNA binding activity. Predicted to be involved in fertilization; gamete generation; and piRNA metabolic process. Predicted to be located in mitochondrion; pi-body; and piP-body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TDRKH	XM_017000123.3	c.*745C>T		3_prime_UTR_variant	14/14		XP_016855612.1
TDRKH	XM_047441989.1	c.*745C>T		3_prime_UTR_variant	14/14		XP_047297945.1
TDRKH	XM_047442008.1	c.*745C>T		3_prime_UTR_variant	14/14		XP_047297964.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAZ3	ENST00000400999.7	c.480-315G>A		intron_variant		5		ENSP00000383784.3
OAZ3	ENST00000453029.2	c.384-315G>A		intron_variant		5		ENSP00000415904.2
OAZ3	ENST00000321531.10	c.345-315G>A		intron_variant		5		ENSP00000313922.5
OAZ3	ENST00000479764.7	c.304-315G>A		intron_variant		5		ENSP00000463055.3
OAZ3	ENST00000635374.1	c.282-1220G>A		intron_variant		5		ENSP00000489420.1
OAZ3	ENST00000635322.1	c.169-315G>A		intron_variant		5		ENSP00000489350.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23427 AN: 152120 Hom.: 1887 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.154 AC: 23456 AN: 152238 Hom.: 1893 Cov.: 32 AF XY: 0.153 AC XY: 11351 AN XY: 74428

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.134

Alfa AF: 0.146 Hom.: 201

Bravo AF: 0.156

Asia WGS AF: 0.127 AC: 441 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.61

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: rs11204884; hg19: chr1-151742333;