10-52586230-C-T

Variant names:

• chr10-52586230-C-T
• rs1919764
• ENST00000443523.3:n.124-25115G>A

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-25115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,566 control chromosomes in the GnomAD database, including 27,285 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 0.60 (27285 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.96-25115G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000443523.3	n.124-25115G>A		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000448017.3	n.222-25115G>A		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000647908.1	n.249-25115G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90447 AN: 151448 Hom.: 27258 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.597 AC: 90531 AN: 151566 Hom.: 27285 Cov.: 32 AF XY: 0.599 AC XY: 44379 AN XY: 74050

African (AFR) AF: 0.533 AC: 22052 AN: 41362

American (AMR) AF: 0.666 AC: 10141 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2540 AN: 3460

East Asian (EAS) AF: 0.540 AC: 2774 AN: 5138

South Asian (SAS) AF: 0.749 AC: 3604 AN: 4810

European-Finnish (FIN) AF: 0.575 AC: 6044 AN: 10516

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41254 AN: 67740

Other (OTH) AF: 0.626 AC: 1319 AN: 2106

Alfa AF: 0.613 Hom.: 46276

Bravo AF: 0.599

Asia WGS AF: 0.697 AC: 2419 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1919764; hg19: chr10-54345990;