rs1445442

chr12-64897514-G-A

Variant summary

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

The NR_033988.1(LINC02389):n.93-3063G>A 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 0.313 in 151,942 control chromosomes in the GnomAD database, including 7,958 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 0.31 (7958 hom., cov: 32)
• Consequence: LINC02389 NR_033988.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

LINC02389 (HGNC:53316): (long intergenic non-protein coding RNA 2389)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02389	NR_033988.1	n.93-3063G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02389	ENST00000662789.1	n.248+12214G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47572 AN: 151824 Hom.: 7954 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47609 AN: 151942 Hom.: 7958 Cov.: 32 AF XY: 0.321 AC XY: 23819 AN XY: 74244

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.310

Alfa AF: 0.326 Hom.: 2929

Bravo AF: 0.305

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.55
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1445442; hg19: chr12-65291294;