rs2009741

Positions:

• chr2-10450263-G-A

Variant summary

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

The NR_110597.1(ODC1-DT):​n.355G>A 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 0.192 in 152,178 control chromosomes in the GnomAD database, including 5,731 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 0.19 (5731 hom., cov: 32)
  • Exomes 𝑓: 0.017 (0 hom.)
• Consequence: ODC1-DT NR_110597.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODC1-DT	NR_110597.1	n.355G>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.1575G>A		non_coding_transcript_exon_variant	1/4	5

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29124 AN: 152000 Hom.: 5712 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.0167 AC: 1 AN: 60 Hom.: 0 Cov.: 0 AF XY: 0.0263 AC XY: 1 AN XY: 38

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.192 AC: 29197 AN: 152118 Hom.: 5731 Cov.: 32 AF XY: 0.198 AC XY: 14742 AN XY: 74380

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0906 Hom.: 417

Bravo AF: 0.207

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009741; hg19: chr2-10590389;