10-52713741-C-T

Variant names:

• chr10-52713741-C-T
• rs10824773
• ENST00000443523.3:n.123+41569G>A

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+41569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,174 control chromosomes in the GnomAD database, including 1,832 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 0.15 (1832 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 4 publications found

Genes affected

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

LOC105378305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.95+41569G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000443523.3	n.123+41569G>A		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000448017.3	n.221+41565G>A		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000647908.1	n.248+10129G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22941 AN: 152056 Hom.: 1830 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.151 AC: 22948 AN: 152174 Hom.: 1832 Cov.: 32 AF XY: 0.151 AC XY: 11233 AN XY: 74402

African (AFR) AF: 0.133 AC: 5518 AN: 41520

American (AMR) AF: 0.120 AC: 1842 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.167 AC: 864 AN: 5174

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1837 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10577 AN: 67994

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.142 Hom.: 272

Bravo AF: 0.143

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs10824773; hg19: chr10-54473501;