rs10878366

Positions:

• chr12-66028594-G-A

Variant summary

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

The NR_146530.1(LINC02425):​n.212C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,080 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC02425 NR_146530.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

Genes affected

LINC02425 (HGNC:53356): (long intergenic non-protein coding RNA 2425)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02425	NR_146530.1	n.212C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02425	ENST00000536217.1	n.212C>T		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42811 AN: 151962 Hom.: 6263 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 AFR exome AF: 0.500

GnomAD4 genome AF: 0.282 AC: 42856 AN: 152078 Hom.: 6282 Cov.: 32 AF XY: 0.278 AC XY: 20703 AN XY: 74342

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.0978

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.314

Alfa AF: 0.314 Hom.: 15687

Bravo AF: 0.284

Asia WGS AF: 0.219 AC: 761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10878366; hg19: chr12-66422374;