NR_186389.1:n.86-12399G>C

Variant names:

• chr10-62277122-G-C
• rs6479800
• NR_186389.1:n.86-12399G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_186389.1(LINC02621):​n.86-12399G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,700 control chromosomes in the GnomAD database, including 7,840 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 0.30 (7840 hom., cov: 31)
• Consequence: LINC02621 NR_186389.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 18 publications found

Genes affected

LINC02621 (HGNC:54098): (long intergenic non-protein coding RNA 2621)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186389.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02621	NR_186389.1		n.86-12399G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45393 AN: 151584 Hom.: 7819 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.300 AC: 45476 AN: 151700 Hom.: 7840 Cov.: 31 AF XY: 0.297 AC XY: 22015 AN XY: 74170

African (AFR) AF: 0.485 AC: 20039 AN: 41298

American (AMR) AF: 0.239 AC: 3642 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.0983 AC: 506 AN: 5148

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4810

European-Finnish (FIN) AF: 0.186 AC: 1962 AN: 10532

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16082 AN: 67890

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.145 Hom.: 249

Bravo AF: 0.304

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.31
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6479800; hg19: chr10-64036881;