rs6432097

Positions:

• chr2-10455452-T-C

Variant summary

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

The NR_110597.1(ODC1-DT):​n.782T>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 0.263 in 169,186 control chromosomes in the GnomAD database, including 6,315 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 0.26 (5669 hom., cov: 32)
  • Exomes 𝑓: 0.28 (646 hom.)
• Consequence: ODC1-DT NR_110597.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODC1-DT	NR_110597.1	n.782T>C		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.2002T>C		non_coding_transcript_exon_variant	4/4	5
ODC1-DT	ENST00000404616.2	n.394T>C		non_coding_transcript_exon_variant	4/4	5
ODC1-DT	ENST00000667698.1	n.366T>C		non_coding_transcript_exon_variant	4/4
ODC1-DT	ENST00000670859.1	n.291T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39616 AN: 151968 Hom.: 5655 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0663

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.284 AC: 4862 AN: 17100 Hom.: 646 Cov.: 0 AF XY: 0.276 AC XY: 2251 AN XY: 8170

Gnomad4 AFR exome AF: 0.440

Gnomad4 AMR exome AF: 0.143

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.383

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.288

GnomAD4 genome AF: 0.261 AC: 39674 AN: 152086 Hom.: 5669 Cov.: 32 AF XY: 0.263 AC XY: 19546 AN XY: 74348

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.234

Alfa AF: 0.231 Hom.: 5761

Bravo AF: 0.256

Asia WGS AF: 0.225 AC: 783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6432097; hg19: chr2-10595578;