chr2-10447043-T-A

Variant names:

• chr2-10447043-T-A
• rs7558559
• NM_002539.3:c.-128+1078A>T

Variant summary

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

The NM_002539.3(ODC1):​c.-128+1078A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,252 control chromosomes in the GnomAD database, including 2,506 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 (2506 hom., cov: 33)
• Consequence: ODC1 NM_002539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 1 publications found

Genes affected

ODC1 (HGNC:8109): (ornithine decarboxylase 1) This gene encodes the rate-limiting enzyme of the polyamine biosynthesis pathway which catalyzes ornithine to putrescine. The activity level for the enzyme varies in response to growth-promoting stimuli and exhibits a high turnover rate in comparison to other mammalian proteins. Originally localized to both chromosomes 2 and 7, the gene encoding this enzyme has been determined to be located on 2p25, with a pseudogene located on 7q31-qter. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Dec 2013]

SNORA80B (HGNC:34355): (small nucleolar RNA, H/ACA box 80B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODC1	NM_002539.3	c.-128+1078A>T		intron_variant	Intron 1 of 11	ENST00000234111.9	NP_002530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9	c.-128+1078A>T		intron_variant	Intron 1 of 11	1	NM_002539.3	ENSP00000234111.4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24108 AN: 152132 Hom.: 2493 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.159 AC: 24165 AN: 152252 Hom.: 2506 Cov.: 33 AF XY: 0.160 AC XY: 11895 AN XY: 74446

African (AFR) AF: 0.279 AC: 11572 AN: 41518

American (AMR) AF: 0.203 AC: 3111 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1097 AN: 5194

South Asian (SAS) AF: 0.102 AC: 494 AN: 4828

European-Finnish (FIN) AF: 0.0883 AC: 936 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6294 AN: 68028

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.127 Hom.: 205

Bravo AF: 0.176

Asia WGS AF: 0.187 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.33
PhyloP100		-0.18
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: rs7558559; hg19: chr2-10587169;