2-10451331-G-C

Position:

• chr2-10451331-G-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.374-950G>C 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 0.58 in 151,544 control chromosomes in the GnomAD database, including 25,963 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 0.58 (25957 hom., cov: 29)
  • Exomes 𝑓: 0.81 (6 hom.)
• Consequence: ODC1-DT NR_110597.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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 = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODC1-DT	NR_110597.1	n.374-950G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODC1-DT	ENST00000553181.6	n.1594-950G>C		intron_variant, non_coding_transcript_variant		5
ODC1-DT	ENST00000667698.1	n.102-950G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87861 AN: 151410 Hom.: 25927 Cov.: 29

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.544

GnomAD4 exome AF: 0.813 AC: 13 AN: 16 Hom.: 6 Cov.: 0 AF XY: 0.875 AC XY: 7 AN XY: 8

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.580 AC: 87933 AN: 151528 Hom.: 25957 Cov.: 29 AF XY: 0.583 AC XY: 43156 AN XY: 74026

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.550

Alfa AF: 0.451 Hom.: 1224

Bravo AF: 0.571

Asia WGS AF: 0.537 AC: 1869 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	0.67
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1728148; hg19: chr2-10591457;