rs1144418

chr12-64899734-T-G

Variant summary

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

The NR_033988.1(LINC02389):n.93-843T>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 0.776 in 152,072 control chromosomes in the GnomAD database, including 46,505 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 0.78 (46505 hom., cov: 31)
• Consequence: LINC02389 NR_033988.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02389	NR_033988.1	n.93-843T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02389	ENST00000662789.1	n.248+14434T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117942 AN: 151954 Hom.: 46449 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.776 AC: 118052 AN: 152072 Hom.: 46505 Cov.: 31 AF XY: 0.776 AC XY: 57676 AN XY: 74306

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.768

Alfa AF: 0.728 Hom.: 82440

Bravo AF: 0.788

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.8
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1144418; hg19: chr12-65293514;