10-52541980-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902426	XR_007062146.1	n.67+8591A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.385+14545T>C		intron_variant	Intron 4 of 6
LNCAROD	ENST00000736176.1	n.322-8596T>C		intron_variant	Intron 4 of 4
LNCAROD	ENST00000736177.1	n.384-8596T>C		intron_variant	Intron 4 of 4
ENSG00000296101	ENST00000736443.1	n.274-37710A>G		intron_variant	Intron 4 of 4

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 v4.3

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;