10-52479886-G-A

Variant names:

• chr10-52479886-G-A
• rs1733731
• ENST00000647908.1:n.386-16554C>T

Variant summary

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

The ENST00000647908.1(LNCAROD):​n.386-16554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,834 control chromosomes in the GnomAD database, including 21,863 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 0.46 (21863 hom., cov: 31)
• Consequence: LNCAROD ENST00000647908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647908.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000647908.1		n.386-16554C>T		intron	N/A
	ENSG00000296101	ENST00000736443.1		n.182+369G>A		intron	N/A
	ENSG00000296101	ENST00000736444.1		n.222+369G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70023 AN: 151716 Hom.: 21807 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.462 AC: 70138 AN: 151834 Hom.: 21863 Cov.: 31 AF XY: 0.464 AC XY: 34404 AN XY: 74194

African (AFR) AF: 0.851 AC: 35267 AN: 41422

American (AMR) AF: 0.443 AC: 6750 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3464

East Asian (EAS) AF: 0.863 AC: 4449 AN: 5158

South Asian (SAS) AF: 0.486 AC: 2334 AN: 4800

European-Finnish (FIN) AF: 0.250 AC: 2642 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16419 AN: 67886

Other (OTH) AF: 0.447 AC: 938 AN: 2100

Alfa AF: 0.292 Hom.: 3685

Bravo AF: 0.491

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1733731; hg19: chr10-54239646;