rs11003107

Positions:

• chr10-52747567-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.95+7743G>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 0.0367 in 152,154 control chromosomes in the GnomAD database, including 240 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 0.037 (240 hom., cov: 33)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378305	NR_155748.1	n.95+7743G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCAROD	ENST00000647908.1	n.99+7739G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5575 AN: 152036 Hom.: 240 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.00976

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00168

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0367 AC: 5580 AN: 152154 Hom.: 240 Cov.: 33 AF XY: 0.0376 AC XY: 2794 AN XY: 74370

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.00956

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.00168

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.00917 Hom.: 43

Bravo AF: 0.0419

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11003107; hg19: chr10-54507327;