rs885815

Positions:

• chr2-10451502-A-G

Variant summary

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

The NR_110597.1(ODC1-DT):​n.374-779A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,176 control chromosomes in the GnomAD database, including 3,677 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 0.21 (3677 hom., cov: 33)
• Consequence: ODC1-DT NR_110597.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODC1-DT	NR_110597.1	n.374-779A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.1594-779A>G		intron_variant, non_coding_transcript_variant		5
ODC1-DT	ENST00000667698.1	n.102-779A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32432 AN: 152058 Hom.: 3675 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.213 AC: 32456 AN: 152176 Hom.: 3677 Cov.: 33 AF XY: 0.215 AC XY: 16000 AN XY: 74398

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.192

Alfa AF: 0.216 Hom.: 1864

Bravo AF: 0.206

Asia WGS AF: 0.113 AC: 394 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	3.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885815; hg19: chr2-10591628;