rs7902708

chr10-52679968-G-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+75342C>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 0.175 in 151,958 control chromosomes in the GnomAD database, including 3,103 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 0.17 (3103 hom., cov: 32)
• Consequence: LOC105378305 NR_155748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

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=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378305	NR_155748.1	n.95+75342C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCAROD	ENST00000647908.1	n.248+43902C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26473 AN: 151838 Hom.: 3089 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.175 AC: 26538 AN: 151958 Hom.: 3103 Cov.: 32 AF XY: 0.175 AC XY: 13027 AN XY: 74282

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.150

Alfa AF: 0.145 Hom.: 272

Bravo AF: 0.177

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	14
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902708; hg19: chr10-54439728;