rs12361072

Variant names:

• chr11-23064665-A-G
• rs12361072
• NR_187205.1:n.625-89925A>G

Variant summary

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

The NR_187205.1(LINC02718):​n.625-89925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 148,124 control chromosomes in the GnomAD database, including 8,702 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 (8702 hom., cov: 29)
• Consequence: LINC02718 NR_187205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820

Genes affected

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

LOC124902646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02718	NR_187205.1	n.625-89925A>G		intron_variant	Intron 4 of 13
LINC02718	NR_187206.1	n.625-90546A>G		intron_variant	Intron 4 of 11
LINC02718	NR_187207.1	n.625-90546A>G		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 45967 AN: 148008 Hom.: 8706 Cov.: 29

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.310 AC: 45974 AN: 148124 Hom.: 8702 Cov.: 29 AF XY: 0.311 AC XY: 22426 AN XY: 72110

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.328

Alfa AF: 0.370 Hom.: 4642

Bravo AF: 0.296

Asia WGS AF: 0.206 AC: 715 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12361072; hg19: chr11-23086211;