10-52610246-A-T

Position:

• chr10-52610246-A-T

Variant summary

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

The NR_155748.1(LOC105378305):​n.96-49131T>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 0.544 in 151,906 control chromosomes in the GnomAD database, including 22,813 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 0.54 (22813 hom., cov: 31)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378305	NR_155748.1	n.96-49131T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCAROD	ENST00000647908.1	n.249-49131T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82513 AN: 151790 Hom.: 22777 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.544 AC: 82611 AN: 151906 Hom.: 22813 Cov.: 31 AF XY: 0.547 AC XY: 40631 AN XY: 74230

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.572

Alfa AF: 0.503 Hom.: 2440

Bravo AF: 0.553

Asia WGS AF: 0.567 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2136892; hg19: chr10-54370006;