rs2222800

Variant names:

• chr10-52582113-A-C
• rs2222800
• ENST00000443523.3:n.124-20998T>G

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-20998T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,048 control chromosomes in the GnomAD database, including 30,018 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 0.63 (30018 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 3 publications found

Genes affected

LNCAROD (HGNC:50913): (lncRNA activating regulator of DKK1)

LOC105378305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443523.3. 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
	LOC105378305	NR_155748.1		n.96-20998T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.124-20998T>G		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.222-20998T>G		intron	N/A
	LNCAROD	ENST00000647908.1		n.249-20998T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95230 AN: 151930 Hom.: 29986 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.627 AC: 95320 AN: 152048 Hom.: 30018 Cov.: 32 AF XY: 0.628 AC XY: 46692 AN XY: 74316

African (AFR) AF: 0.620 AC: 25715 AN: 41486

American (AMR) AF: 0.677 AC: 10355 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3014 AN: 5162

South Asian (SAS) AF: 0.762 AC: 3673 AN: 4820

European-Finnish (FIN) AF: 0.577 AC: 6078 AN: 10534

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41764 AN: 67962

Other (OTH) AF: 0.646 AC: 1364 AN: 2112

Alfa AF: 0.596 Hom.: 3568

Bravo AF: 0.632

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.98

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: rs2222800;

hg19: chr10-54341873;