rs2569991

chr3-12881698-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136189.1(LINC02022):n.354-2705G>T variant causes a intron, non coding transcript 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 NR_136189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

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

LOC105376956 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02022	NR_136189.1	n.354-2705G>T		intron_variant, non_coding_transcript_variant
LOC105376956	XR_940599.2	n.1913-380C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02022	ENST00000448129.1	n.354-2705G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.701

Alfa AF: 0.746 Hom.: 54611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569991; hg19: chr3-12923197;