rs2357551

Variant names:

• chr2-10452054-C-T
• rs2357551
• ENST00000810678.1:n.535G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000810678.1(ENSG00000305382):​n.535G>A 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 0.316 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: ENSG00000305382 ENST00000810678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 2 publications found

Genes affected

ENSG00000305382 (HGNC:):

ODC1-DT (HGNC:54070): (ODC1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810678.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODC1-DT	NR_110597.1		n.374-227C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305382	ENST00000810678.1		n.535G>A		non_coding_transcript_exon	Exon 2 of 2
	ODC1-DT	ENST00000553181.6	TSL:5	n.1594-227C>T		intron	N/A
	ODC1-DT	ENST00000667698.2		n.104-227C>T		intron	N/A

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

African (AFR) AF: 0.254 AC: 10540 AN: 41526

American (AMR) AF: 0.350 AC: 5344 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1482 AN: 5184

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3485 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23459 AN: 67988

Other (OTH) AF: 0.308 AC: 651 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.72
PhyloP100		0.057

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2357551;

hg19: chr2-10592180;