10-52464217-A-G

Variant names:

• chr10-52464217-A-G
• rs1733724
• ENST00000422763.1:n.138-885T>C

Variant summary

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

The ENST00000422763.1(LNCAROD):​n.138-885T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,132 control chromosomes in the GnomAD database, including 51,241 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 0.81 (51241 hom., cov: 32)
• Consequence: LNCAROD ENST00000422763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 34 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 (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCAROD	NR_120641.1	n.138-885T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000422763.1	n.138-885T>C		intron_variant	Intron 1 of 3	3
LNCAROD	ENST00000647908.1	n.386-885T>C		intron_variant	Intron 4 of 6
ENSG00000296101	ENST00000736443.1	n.136+10912A>G		intron_variant	Intron 2 of 4
ENSG00000296101	ENST00000736444.1	n.176+10912A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123842 AN: 152014 Hom.: 51183 Cov.: 32

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.815 AC: 123955 AN: 152132 Hom.: 51241 Cov.: 32 AF XY: 0.813 AC XY: 60484 AN XY: 74364

African (AFR) AF: 0.954 AC: 39642 AN: 41534

American (AMR) AF: 0.772 AC: 11795 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4874 AN: 5158

South Asian (SAS) AF: 0.739 AC: 3566 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8005 AN: 10564

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.752 AC: 51136 AN: 67976

Other (OTH) AF: 0.796 AC: 1682 AN: 2114

Alfa AF: 0.774 Hom.: 161997

Bravo AF: 0.820

Asia WGS AF: 0.871 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.82
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1733724; hg19: chr10-54223977;