chr10-52591345-T-C

Variant names:

• chr10-52591345-T-C
• rs1919738
• ENST00000443523.3:n.124-30230A>G

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-30230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,928 control chromosomes in the GnomAD database, including 29,422 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 0.62 (29422 hom., cov: 31)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 3 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=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 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.96-30230A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.124-30230A>G		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.222-30230A>G		intron	N/A
	LNCAROD	ENST00000647908.1		n.249-30230A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94211 AN: 151810 Hom.: 29395 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.621 AC: 94294 AN: 151928 Hom.: 29422 Cov.: 31 AF XY: 0.622 AC XY: 46196 AN XY: 74268

African (AFR) AF: 0.606 AC: 25090 AN: 41392

American (AMR) AF: 0.676 AC: 10324 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2938 AN: 5114

South Asian (SAS) AF: 0.754 AC: 3636 AN: 4822

European-Finnish (FIN) AF: 0.575 AC: 6077 AN: 10560

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41523 AN: 67976

Other (OTH) AF: 0.643 AC: 1356 AN: 2110

Alfa AF: 0.620 Hom.: 22140

Bravo AF: 0.625

Asia WGS AF: 0.711 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.027
DANN	Benign	0.19
PhyloP100		-3.1

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: rs1919738;

hg19: chr10-54351105;