rs1733724

Positions:

• chr10-52464217-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120641.1(LNCAROD):​n.138-885T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,132 control chromosomes in the GnomAD database, including 51,241 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 0.81 (51241 hom., cov: 32)
• Consequence: LNCAROD NR_120641.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

LNCAROD (HGNC:50913): (lncRNA activating regulator of DKK1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNCAROD	NR_120641.1	n.138-885T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.386-885T>C		intron_variant, non_coding_transcript_variant
LNCAROD	ENST00000422763.1	n.138-885T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123842 AN: 152014 Hom.: 51183 Cov.: 32

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.815 AC: 123955 AN: 152132 Hom.: 51241 Cov.: 32 AF XY: 0.813 AC XY: 60484 AN XY: 74364

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.796

Alfa AF: 0.764 Hom.: 69831

Bravo AF: 0.820

Asia WGS AF: 0.871 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1733724; hg19: chr10-54223977;