rs17587392

Variant names:

• chr10-52751488-T-C
• rs17587392
• ENST00000443523.3:n.123+3822A>G

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+3822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 152,176 control chromosomes in the GnomAD database, including 453 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 0.072 (453 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0869 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.95+3822A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.123+3822A>G		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.221+3818A>G		intron	N/A
	LNCAROD	ENST00000647908.1		n.99+3818A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10932 AN: 152060 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0719 AC: 10944 AN: 152176 Hom.: 453 Cov.: 32 AF XY: 0.0707 AC XY: 5258 AN XY: 74396

African (AFR) AF: 0.0585 AC: 2430 AN: 41522

American (AMR) AF: 0.0559 AC: 855 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3466

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5172

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4826

European-Finnish (FIN) AF: 0.0942 AC: 997 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6037 AN: 67994

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0724 Hom.: 138

Bravo AF: 0.0686

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17587392;

hg19: chr10-54511248;