ENST00000647908.1:n.385+14545T>C

Variant names:

• chr10-52541980-A-G
• rs7085224
• ENST00000647908.1:n.385+14545T>C

Variant summary

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

The ENST00000647908.1(LNCAROD):​n.385+14545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,768 control chromosomes in the GnomAD database, including 10,686 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 0.33 (10686 hom., cov: 30)
• Consequence: LNCAROD ENST00000647908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 3 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=-0.83).
• 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: ENST00000647908.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000647908.1		n.385+14545T>C		intron	N/A
	LNCAROD	ENST00000736176.1		n.322-8596T>C		intron	N/A
	LNCAROD	ENST00000736177.1		n.384-8596T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49318 AN: 151650 Hom.: 10661 Cov.: 30

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.325 AC: 49396 AN: 151768 Hom.: 10686 Cov.: 30 AF XY: 0.334 AC XY: 24804 AN XY: 74168

African (AFR) AF: 0.506 AC: 20926 AN: 41352

American (AMR) AF: 0.380 AC: 5788 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3458

East Asian (EAS) AF: 0.893 AC: 4566 AN: 5112

South Asian (SAS) AF: 0.465 AC: 2232 AN: 4800

European-Finnish (FIN) AF: 0.250 AC: 2636 AN: 10562

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11700 AN: 67948

Other (OTH) AF: 0.295 AC: 621 AN: 2106

Alfa AF: 0.226 Hom.: 22609

Bravo AF: 0.345

Asia WGS AF: 0.683 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs7085224; hg19: chr10-54301740;