chr2-10452054-C-T

Position:

• chr2-10452054-C-T

Variant summary

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

The NR_110597.1(ODC1-DT):​n.374-227C>T 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 0.316 in 152,170 control chromosomes in the GnomAD database, including 7,823 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 0.32 (7823 hom., cov: 33)
• Consequence: ODC1-DT NR_110597.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODC1-DT	NR_110597.1	n.374-227C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.1594-227C>T		intron_variant, non_coding_transcript_variant		5
ODC1-DT	ENST00000667698.1	n.102-227C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47997 AN: 152052 Hom.: 7815 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.316 AC: 48025 AN: 152170 Hom.: 7823 Cov.: 33 AF XY: 0.314 AC XY: 23392 AN XY: 74406

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.308

Alfa AF: 0.327 Hom.: 1550

Bravo AF: 0.313

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357551; hg19: chr2-10592180;