10-52610246-A-T

Variant names:

• chr10-52610246-A-T
• rs2136892
• ENST00000443523.3:n.124-49131T>A

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-49131T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,906 control chromosomes in the GnomAD database, including 22,813 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 0.54 (22813 hom., cov: 31)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443523.3. 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
	LOC105378305	NR_155748.1		n.96-49131T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.124-49131T>A		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.222-49131T>A		intron	N/A
	LNCAROD	ENST00000647908.1		n.249-49131T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82513 AN: 151790 Hom.: 22777 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.544 AC: 82611 AN: 151906 Hom.: 22813 Cov.: 31 AF XY: 0.547 AC XY: 40631 AN XY: 74230

African (AFR) AF: 0.617 AC: 25542 AN: 41430

American (AMR) AF: 0.610 AC: 9310 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1916 AN: 3466

East Asian (EAS) AF: 0.402 AC: 2072 AN: 5148

South Asian (SAS) AF: 0.606 AC: 2915 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5277 AN: 10556

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33728 AN: 67930

Other (OTH) AF: 0.572 AC: 1208 AN: 2112

Alfa AF: 0.503 Hom.: 2440

Bravo AF: 0.553

Asia WGS AF: 0.567 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2136892; hg19: chr10-54370006;