rs1348350

Variant names:

• chr10-52650442-C-A
• rs1348350
• ENST00000443523.3:n.124-89327G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-52650442-C-A
• chr10-52650442-C-G
• chr10-52650442-C-T

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.124-89327G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 152,138 control chromosomes in the GnomAD database, including 57,477 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 0.86 (57477 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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.96-89327G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.124-89327G>T		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.222-89327G>T		intron	N/A
	LNCAROD	ENST00000647908.1		n.248+73428G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131472 AN: 152020 Hom.: 57441 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.865 AC: 131563 AN: 152138 Hom.: 57477 Cov.: 32 AF XY: 0.869 AC XY: 64657 AN XY: 74392

African (AFR) AF: 0.730 AC: 30284 AN: 41464

American (AMR) AF: 0.915 AC: 13986 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3167 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4970 AN: 5166

South Asian (SAS) AF: 0.856 AC: 4133 AN: 4826

European-Finnish (FIN) AF: 0.948 AC: 10054 AN: 10602

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 61994 AN: 68010

Other (OTH) AF: 0.890 AC: 1877 AN: 2108

Alfa AF: 0.897 Hom.: 102059

Bravo AF: 0.856

Asia WGS AF: 0.886 AC: 3081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.055

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: rs1348350;

hg19: chr10-54410202;