rs1733731

Variant names:

• chr10-52479886-G-A
• rs1733731
• ENST00000647908.1:n.386-16554C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-52479886-G-A
• chr10-52479886-G-C
• chr10-52479886-G-T

Variant summary

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

The ENST00000647908.1(LNCAROD):​n.386-16554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,834 control chromosomes in the GnomAD database, including 21,863 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 0.46 (21863 hom., cov: 31)
• Consequence: LNCAROD ENST00000647908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.386-16554C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70023 AN: 151716 Hom.: 21807 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.462 AC: 70138 AN: 151834 Hom.: 21863 Cov.: 31 AF XY: 0.464 AC XY: 34404 AN XY: 74194

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.447

Alfa AF: 0.306 Hom.: 2188

Bravo AF: 0.491

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1733731; hg19: chr10-54239646;