chr10-52586230-C-T

Position:

• chr10-52586230-C-T

Variant summary

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

The NR_155748.1(LOC105378305):​n.96-25115G>A 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 0.597 in 151,566 control chromosomes in the GnomAD database, including 27,285 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 0.60 (27285 hom., cov: 32)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

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

LOC105378305 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.96-25115G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.249-25115G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90447 AN: 151448 Hom.: 27258 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.597 AC: 90531 AN: 151566 Hom.: 27285 Cov.: 32 AF XY: 0.599 AC XY: 44379 AN XY: 74050

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.626

Alfa AF: 0.614 Hom.: 36298

Bravo AF: 0.599

Asia WGS AF: 0.697 AC: 2419 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919764; hg19: chr10-54345990;