10-52679968-G-C

Variant names:

• chr10-52679968-G-C
• rs7902708
• ENST00000443523.3:n.123+75342C>G

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+75342C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,958 control chromosomes in the GnomAD database, including 3,103 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 0.17 (3103 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• Publications: 13 publications found

Genes affected

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

ENSG00000296123 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.95+75342C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000443523.3	n.123+75342C>G		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000448017.3	n.221+75338C>G		intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000647908.1	n.248+43902C>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26473 AN: 151838 Hom.: 3089 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.175 AC: 26538 AN: 151958 Hom.: 3103 Cov.: 32 AF XY: 0.175 AC XY: 13027 AN XY: 74282

African (AFR) AF: 0.323 AC: 13363 AN: 41420

American (AMR) AF: 0.122 AC: 1865 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5172

South Asian (SAS) AF: 0.131 AC: 631 AN: 4804

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10548

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7351 AN: 67952

Other (OTH) AF: 0.150 AC: 317 AN: 2112

Alfa AF: 0.145 Hom.: 272

Bravo AF: 0.177

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.59
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs7902708; hg19: chr10-54439728;