rs2286983

Variant names:

• chr3-172574694-G-A
• rs2286983
• ENST00000424941.3:n.327-354C>T

Variant summary

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

The ENST00000424941.3(LINC02068):​n.327-354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,138 control chromosomes in the GnomAD database, including 6,853 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 0.29 (6853 hom., cov: 32)
• Consequence: LINC02068 ENST00000424941.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

Genes affected

LINC02068 (HGNC:52914): (long intergenic non-protein coding RNA 2068)

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 (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02068	NR_146714.1	n.327-354C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02068	ENST00000424941.3	n.327-354C>T		intron_variant	Intron 2 of 3	2
LINC02068	ENST00000441185.7	n.276-13625C>T		intron_variant	Intron 2 of 2	3
LINC02068	ENST00000830139.1	n.234+19767C>T		intron_variant	Intron 2 of 2
LINC02068	ENST00000830140.1	n.419-354C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43788 AN: 152020 Hom.: 6826 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.288 AC: 43868 AN: 152138 Hom.: 6853 Cov.: 32 AF XY: 0.289 AC XY: 21472 AN XY: 74376

African (AFR) AF: 0.411 AC: 17046 AN: 41510

American (AMR) AF: 0.233 AC: 3555 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1713 AN: 5174

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2954 AN: 10562

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15721 AN: 67990

Other (OTH) AF: 0.258 AC: 546 AN: 2116

Alfa AF: 0.247 Hom.: 20854

Bravo AF: 0.292

Asia WGS AF: 0.312 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.55
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2286983; hg19: chr3-172292484;