10-52668065-T-G

Variant names:

• chr10-52668065-T-G
• rs1373004
• ENST00000443523.3:n.123+87245A>C

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+87245A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,022 control chromosomes in the GnomAD database, including 46,825 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 0.76 (46825 hom., cov: 31)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672
• Publications: 31 publications found

Genes affected

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

ENSG00000296123 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 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.95+87245A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.123+87245A>C		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.221+87241A>C		intron	N/A
	LNCAROD	ENST00000647908.1		n.248+55805A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115549 AN: 151902 Hom.: 46824 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.760 AC: 115574 AN: 152022 Hom.: 46825 Cov.: 31 AF XY: 0.762 AC XY: 56586 AN XY: 74298

African (AFR) AF: 0.452 AC: 18739 AN: 41436

American (AMR) AF: 0.839 AC: 12822 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3153 AN: 3472

East Asian (EAS) AF: 0.803 AC: 4154 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4191 AN: 4816

European-Finnish (FIN) AF: 0.844 AC: 8905 AN: 10556

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60726 AN: 67976

Other (OTH) AF: 0.810 AC: 1711 AN: 2112

Alfa AF: 0.863 Hom.: 117771

Bravo AF: 0.747

Asia WGS AF: 0.791 AC: 2746 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.79
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1373004; hg19: chr10-54427825;