10-52591345-T-C

Position:

• chr10-52591345-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.96-30230A>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 0.621 in 151,928 control chromosomes in the GnomAD database, including 29,422 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 0.62 (29422 hom., cov: 31)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

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=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.96-30230A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.249-30230A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94211 AN: 151810 Hom.: 29395 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.621 AC: 94294 AN: 151928 Hom.: 29422 Cov.: 31 AF XY: 0.622 AC XY: 46196 AN XY: 74268

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.643

Alfa AF: 0.622 Hom.: 15766

Bravo AF: 0.625

Asia WGS AF: 0.711 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.027
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919738; hg19: chr10-54351105;