rs12413153

Positions:

• chr10-91055067-T-G

Variant summary

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

The NR_047467.2(LINC00502):​n.360-6912T>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 0.119 in 371,842 control chromosomes in the GnomAD database, including 3,402 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 0.10 (1149 hom., cov: 33)
  • Exomes 𝑓: 0.13 (2253 hom.)
• Consequence: LINC00502 NR_047467.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

LINC00502 (HGNC:43442): (long intergenic non-protein coding RNA 502)

DDX18P6 (HGNC:31126): (DEAD-box helicase 18 pseudogene 6)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00502	NR_047467.2	n.360-6912T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00502	ENST00000423621.2	n.815-6912T>G		intron_variant, non_coding_transcript_variant		3
DDX18P6	ENST00000450119.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15977 AN: 152116 Hom.: 1150 Cov.: 33

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.128 AC: 28135 AN: 219608 Hom.: 2253 Cov.: 0 AF XY: 0.126 AC XY: 15595 AN XY: 123430

Gnomad4 AFR exome AF: 0.0441

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.312

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.105 AC: 15972 AN: 152234 Hom.: 1149 Cov.: 33 AF XY: 0.110 AC XY: 8165 AN XY: 74428

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0940 Hom.: 231

Bravo AF: 0.113

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12413153; hg19: chr10-92814824;