12-20015153-T-C

Variant summary

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

The NR_040098.1(LINC02398):n.344+125T>C 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 0.636 in 151,944 control chromosomes in the GnomAD database, including 33,163 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 0.64 (33158 hom., cov: 31)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: LINC02398 NR_040098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

Genes affected

LINC02398 (HGNC:53325): (long intergenic non-protein coding RNA 2398)

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 (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02398	NR_040098.1	n.344+125T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02398	ENST00000536666.1	n.249+125T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96619 AN: 151816 Hom.: 33146 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 AF XY: 1.00 AC XY: 10 AN XY: 10

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.636 AC: 96657 AN: 151934 Hom.: 33158 Cov.: 31 AF XY: 0.639 AC XY: 47420 AN XY: 74252

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.624

Alfa AF: 0.646 Hom.: 2432

Bravo AF: 0.615

Asia WGS AF: 0.562 AC: 1958 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	1.3
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505843; hg19: chr12-20168087;