rs1194742

chr10-52453790-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.366+796T>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 0.118 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 NR_120641.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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 = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LNCAROD	NR_120641.1	n.366+796T>C		intron_variant, non_coding_transcript_variant
LNCAROD	NR_120642.1	n.331+796T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCAROD	ENST00000435813.6	n.331+796T>C		intron_variant, non_coding_transcript_variant		1
LNCAROD	ENST00000647908.1	n.614+796T>C		intron_variant, non_coding_transcript_variant
LNCAROD	ENST00000422763.1	n.366+796T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0371

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0620 Hom.: 964

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1194742; hg19: chr10-54213550;