NR_187286.1:n.1496G>A

Variant names:

• chr1-208636753-C-T
• rs1166864
• NR_187286.1:n.1496G>A

Variant summary

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

The NR_187286.1(LINC02769):​n.1496G>A 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 0.557 in 151,994 control chromosomes in the GnomAD database, including 23,655 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 0.56 (23655 hom., cov: 32)
• Consequence: LINC02769 NR_187286.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 2 publications found

Genes affected

LINC02769 (HGNC:54289): (long intergenic non-protein coding RNA 2769)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187286.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02769	NR_187286.1		n.1496G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84564 AN: 151876 Hom.: 23625 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.557 AC: 84636 AN: 151994 Hom.: 23655 Cov.: 32 AF XY: 0.561 AC XY: 41697 AN XY: 74292

African (AFR) AF: 0.569 AC: 23553 AN: 41426

American (AMR) AF: 0.604 AC: 9240 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1942 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2684 AN: 5170

South Asian (SAS) AF: 0.575 AC: 2761 AN: 4804

European-Finnish (FIN) AF: 0.607 AC: 6399 AN: 10548

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36209 AN: 67964

Other (OTH) AF: 0.540 AC: 1140 AN: 2112

Alfa AF: 0.539 Hom.: 29635

Bravo AF: 0.561

Asia WGS AF: 0.558 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1166864; hg19: chr1-208810098;