rs764377

Positions:

• chr12-127897105-C-T

Variant summary

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

The NR_033987.1(LINC02393):​n.486C>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 0.215 in 152,168 control chromosomes in the GnomAD database, including 5,302 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 0.21 (5302 hom., cov: 33)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: LINC02393 NR_033987.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

LINC02393 (HGNC:53320): (long intergenic non-protein coding RNA 2393)

LINC00508 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02393	NR_033987.1	n.486C>T		non_coding_transcript_exon_variant	3/3
LINC00508	NR_126452.2	n.312-12000G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02393	ENST00000662498.1	n.393C>T		non_coding_transcript_exon_variant	2/2
LINC02393	ENST00000614177.2	n.459C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32639 AN: 152016 Hom.: 5298 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.176 AC: 6 AN: 34 Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.143

GnomAD4 genome AF: 0.215 AC: 32672 AN: 152134 Hom.: 5302 Cov.: 33 AF XY: 0.214 AC XY: 15904 AN XY: 74376

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.188

Alfa AF: 0.145 Hom.: 638

Bravo AF: 0.228

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764377; hg19: chr12-128381650;