chr3-27683361-G-A

Variant names:

• chr3-27683361-G-A
• rs2724509
• ENST00000785157.1:n.91+5452G>A

Variant summary

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

The ENST00000785157.1(LINC02084):​n.91+5452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,122 control chromosomes in the GnomAD database, including 1,563 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 0.13 (1563 hom., cov: 32)
• Consequence: LINC02084 ENST00000785157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 8 publications found

Genes affected

LINC02084 (HGNC:52934): (long intergenic non-protein coding RNA 2084)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785157.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02084	ENST00000785157.1		n.91+5452G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20142 AN: 152004 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.132 AC: 20145 AN: 152122 Hom.: 1563 Cov.: 32 AF XY: 0.129 AC XY: 9600 AN XY: 74356

African (AFR) AF: 0.0574 AC: 2383 AN: 41546

American (AMR) AF: 0.132 AC: 2014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3468

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5180

South Asian (SAS) AF: 0.0605 AC: 292 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1684 AN: 10552

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12386 AN: 67958

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.165 Hom.: 9753

Bravo AF: 0.129

Asia WGS AF: 0.0420 AC: 145 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2724509; hg19: chr3-27724852;