rs10878366

Variant names:

• chr12-66028594-G-A
• rs10878366
• ENST00000536217.1:n.212C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536217.1(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 ENST00000536217.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536217.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02425	NR_146530.1		n.212C>T		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02425	ENST00000536217.1	TSL:3	n.212C>T		non_coding_transcript_exon	Exon 2 of 3
	LINC02425	ENST00000763732.1		n.157C>T		non_coding_transcript_exon	Exon 2 of 3
	LINC02425	ENST00000763733.1		n.242C>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.245 AC: 10152 AN: 41478

American (AMR) AF: 0.292 AC: 4468 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1438 AN: 3472

East Asian (EAS) AF: 0.0978 AC: 506 AN: 5176

South Asian (SAS) AF: 0.266 AC: 1281 AN: 4812

European-Finnish (FIN) AF: 0.233 AC: 2459 AN: 10572

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21436 AN: 67978

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.306 Hom.: 31041

Bravo AF: 0.284

Asia WGS AF: 0.219 AC: 761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10878366; hg19: chr12-66422374; COSMIC: COSV108274733;