rs11003107

Variant names:

• chr10-52747567-C-T
• rs11003107
• ENST00000443523.3:n.123+7743G>A

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+7743G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,154 control chromosomes in the GnomAD database, including 240 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 0.037 (240 hom., cov: 33)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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+7743G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.123+7743G>A		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.221+7739G>A		intron	N/A
	LNCAROD	ENST00000647908.1		n.99+7739G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5575 AN: 152036 Hom.: 240 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.00976

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00168

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0367 AC: 5580 AN: 152154 Hom.: 240 Cov.: 33 AF XY: 0.0376 AC XY: 2794 AN XY: 74370

African (AFR) AF: 0.0928 AC: 3849 AN: 41490

American (AMR) AF: 0.0323 AC: 493 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.135 AC: 700 AN: 5172

South Asian (SAS) AF: 0.00956 AC: 46 AN: 4812

European-Finnish (FIN) AF: 0.0270 AC: 286 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00168 AC: 114 AN: 68012

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0132 Hom.: 82

Bravo AF: 0.0419

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.48

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: rs11003107;

hg19: chr10-54507327;