chr2-10452046-A-G

Position:

• chr2-10452046-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.374-235A>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 0.0506 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: ODC1-DT NR_110597.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

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=-0.88).
• 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/exons	MANE	Protein	UniProt
ODC1-DT	NR_110597.1	n.374-235A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.1594-235A>G		intron_variant, non_coding_transcript_variant		5
ODC1-DT	ENST00000667698.1	n.102-235A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0675 Hom.: 102

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2884211; hg19: chr2-10592172;