chr10-52453790-A-G

Variant names:

• chr10-52453790-A-G
• rs1194742
• ENST00000435813.7:n.385+796T>C

Variant summary

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

The ENST00000435813.7(LNCAROD):​n.385+796T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,220 control chromosomes in the GnomAD database, including 1,688 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 0.12 (1688 hom., cov: 32)
• Consequence: LNCAROD ENST00000435813.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 3 publications found

Genes affected

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

ENSG00000296101 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCAROD	NR_120641.1	n.366+796T>C		intron_variant	Intron 3 of 3
LNCAROD	NR_120642.1	n.331+796T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000435813.7	n.385+796T>C		intron_variant	Intron 2 of 2	1
LNCAROD	ENST00000422763.1	n.366+796T>C		intron_variant	Intron 3 of 3	3
LNCAROD	ENST00000647908.1	n.614+796T>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17895 AN: 152102 Hom.: 1681 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0371

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.118 AC: 17927 AN: 152220 Hom.: 1688 Cov.: 32 AF XY: 0.120 AC XY: 8908 AN XY: 74432

African (AFR) AF: 0.229 AC: 9502 AN: 41504

American (AMR) AF: 0.185 AC: 2823 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.170 AC: 877 AN: 5174

South Asian (SAS) AF: 0.156 AC: 751 AN: 4822

European-Finnish (FIN) AF: 0.0371 AC: 394 AN: 10624

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0428 AC: 2909 AN: 68016

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.0684 Hom.: 2563

Bravo AF: 0.129

Asia WGS AF: 0.208 AC: 723 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	1.7
DANN	Benign	0.51
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1194742; hg19: chr10-54213550;