rs2569991

Variant names:

• chr3-12881698-C-A
• rs2569991
• ENST00000448129.2:n.354-2705G>T

Variant summary

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

The ENST00000448129.2(LINC02022):​n.354-2705G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,166 control chromosomes in the GnomAD database, including 39,560 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 0.72 (39560 hom., cov: 33)
• Consequence: LINC02022 ENST00000448129.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 5 publications found

Genes affected

LINC02022 (HGNC:52857): (long intergenic non-protein coding RNA 2022)

LOC105376956 (HGNC:):

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 = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02022	NR_136189.1	n.354-2705G>T		intron_variant	Intron 1 of 2
LOC105376956	XR_940599.2	n.1913-380C>A		intron_variant	Intron 3 of 5
LOC105376956	XR_940600.2	n.467-380C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02022	ENST00000448129.2	n.354-2705G>T		intron_variant	Intron 1 of 2	2
LINC02022	ENST00000748308.1	n.90+3161G>T		intron_variant	Intron 1 of 3
LINC02022	ENST00000748309.1	n.87+3161G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109137 AN: 152048 Hom.: 39533 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.718 AC: 109200 AN: 152166 Hom.: 39560 Cov.: 33 AF XY: 0.713 AC XY: 53037 AN XY: 74388

African (AFR) AF: 0.708 AC: 29386 AN: 41506

American (AMR) AF: 0.659 AC: 10067 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2100 AN: 5176

South Asian (SAS) AF: 0.659 AC: 3179 AN: 4822

European-Finnish (FIN) AF: 0.742 AC: 7866 AN: 10604

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51832 AN: 67998

Other (OTH) AF: 0.701 AC: 1480 AN: 2112

Alfa AF: 0.744 Hom.: 69512

Bravo AF: 0.711

Asia WGS AF: 0.548 AC: 1908 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	0.86
DANN	Benign	0.25
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2569991; hg19: chr3-12923197;