rs2282

chr8-136106932-G-Achr8-136106932-G-T

Variant summary

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

The ENST00000502901.6(LINC02055):n.186-55543G>A 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 0.505 in 152,010 control chromosomes in the GnomAD database, including 20,065 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 0.50 (20065 hom., cov: 33)
• Consequence: LINC02055 ENST00000502901.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000502901.6	n.186-55543G>A		intron_variant, non_coding_transcript_variant		4
LINC02055	ENST00000523150.1	n.330+17726G>A		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000648077.2	n.283+17726G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76638 AN: 151892 Hom.: 20045 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.505 AC: 76700 AN: 152010 Hom.: 20065 Cov.: 33 AF XY: 0.511 AC XY: 37954 AN XY: 74288

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.520

Alfa AF: 0.390 Hom.: 1376

Bravo AF: 0.516

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.77
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282; hg19: chr8-137119175;