rs2884211

Variant names:

• chr2-10452046-A-G
• rs2884211
• ENST00000810678.1:n.543T>C

Variant summary

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

The ENST00000810678.1(ENSG00000305382):​n.543T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,318 control chromosomes in the GnomAD database, including 263 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 0.051 (263 hom., cov: 33)
• Consequence: ENSG00000305382 ENST00000810678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 1 publications found

Genes affected

ENSG00000305382 (HGNC:):

ODC1-DT (HGNC:54070): (ODC1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODC1-DT	NR_110597.1	n.374-235A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305382	ENST00000810678.1	n.543T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ODC1-DT	ENST00000553181.6	n.1594-235A>G		intron_variant	Intron 1 of 3	5
ODC1-DT	ENST00000667698.2	n.104-235A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7713 AN: 152200 Hom.: 264 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0755

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0506 AC: 7706 AN: 152318 Hom.: 263 Cov.: 33 AF XY: 0.0495 AC XY: 3688 AN XY: 74482

African (AFR) AF: 0.0140 AC: 580 AN: 41576

American (AMR) AF: 0.0491 AC: 750 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.0702 AC: 339 AN: 4832

European-Finnish (FIN) AF: 0.0449 AC: 477 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0755 AC: 5133 AN: 68026

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0560 Hom.: 157

Bravo AF: 0.0476

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0040
DANN	Benign	0.24
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2884211; hg19: chr2-10592172;