rs12882548

Positions:

• chr14-26797775-T-C
• chr14-26797775-T-G

Variant summary

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

The NR_110033.1(LINC02294):​n.305+10947A>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 0.243 in 152,130 control chromosomes in the GnomAD database, including 4,673 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 0.24 (4673 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02294 NR_110033.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

LINC02294 (HGNC:53210): (long intergenic non-protein coding RNA 2294)

(HGNC:):

NOVA1-DT (HGNC:19827): (NOVA1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02294	NR_110033.1	n.305+10947A>G		intron_variant, non_coding_transcript_variant
NOVA1-DT	NR_147061.1	n.2021-8461T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02294	ENST00000549330.1	n.292+10947A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000656336.1	n.480+72981T>C		intron_variant, non_coding_transcript_variant
NOVA1-DT	ENST00000662478.1	n.1778-8461T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36888 AN: 152012 Hom.: 4669 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.208

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.243 AC: 36917 AN: 152130 Hom.: 4673 Cov.: 32 AF XY: 0.244 AC XY: 18129 AN XY: 74374

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.215

Alfa AF: 0.251 Hom.: 6578

Bravo AF: 0.230

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12882548; hg19: chr14-27266981;