10-52573815-T-C

Variant names:

• chr10-52573815-T-C
• rs1881747
• ENST00000443523.3:n.124-12700A>G

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-12700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,014 control chromosomes in the GnomAD database, including 9,245 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 0.30 (9245 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 publications found

Genes affected

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

ENSG00000296101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378305	NR_155748.1		n.96-12700A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.124-12700A>G		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.222-12700A>G		intron	N/A
	LNCAROD	ENST00000647908.1		n.249-12700A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46285 AN: 151896 Hom.: 9224 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.305 AC: 46352 AN: 152014 Hom.: 9245 Cov.: 32 AF XY: 0.314 AC XY: 23341 AN XY: 74294

African (AFR) AF: 0.433 AC: 17944 AN: 41438

American (AMR) AF: 0.380 AC: 5804 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4592 AN: 5140

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2631 AN: 10592

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11672 AN: 67966

Other (OTH) AF: 0.288 AC: 609 AN: 2112

Alfa AF: 0.221 Hom.: 3812

Bravo AF: 0.321

Asia WGS AF: 0.681 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1881747; hg19: chr10-54333575;