chr10-52662578-C-T

Position:

• chr10-52662578-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_155748.1(LOC105378305):​n.95+92732G>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 0.265 in 152,064 control chromosomes in the GnomAD database, including 6,339 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 0.27 (6339 hom., cov: 32)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.968

Genes affected

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

LOC105378305 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378305	NR_155748.1	n.95+92732G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCAROD	ENST00000647908.1	n.248+61292G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40373 AN: 151946 Hom.: 6347 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.265 AC: 40368 AN: 152064 Hom.: 6339 Cov.: 32 AF XY: 0.263 AC XY: 19540 AN XY: 74338

Gnomad4 AFR AF: 0.0968

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.248

Alfa AF: 0.329 Hom.: 11675

Bravo AF: 0.261

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
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: rs10762864; hg19: chr10-54422338;