rs17587392

Positions:

• chr10-52751488-T-C

Variant summary

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

The NR_155748.1(LOC105378305):​n.95+3822A>G 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 0.0719 in 152,176 control chromosomes in the GnomAD database, including 453 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 0.072 (453 hom., cov: 32)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.95+3822A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.99+3818A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10932 AN: 152060 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0719 AC: 10944 AN: 152176 Hom.: 453 Cov.: 32 AF XY: 0.0707 AC XY: 5258 AN XY: 74396

Gnomad4 AFR AF: 0.0585

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.0888

Gnomad4 OTH AF: 0.0796

Alfa AF: 0.0757 Hom.: 67

Bravo AF: 0.0686

Asia WGS AF: 0.0230 AC: 81 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	2.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17587392; hg19: chr10-54511248;