rs1031282

Variant names:

• chr8-136042414-G-A
• rs1031282
• ENST00000650054.1:n.250+30227G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-136042414-G-A
• chr8-136042414-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000650054.1(LINC02055):​n.250+30227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,646 control chromosomes in the GnomAD database, including 7,718 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 0.31 (7718 hom., cov: 31)
• Consequence: LINC02055 ENST00000650054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650054.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000650054.1		n.250+30227G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47628 AN: 151528 Hom.: 7713 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.314 AC: 47657 AN: 151646 Hom.: 7718 Cov.: 31 AF XY: 0.318 AC XY: 23578 AN XY: 74070

African (AFR) AF: 0.250 AC: 10326 AN: 41356

American (AMR) AF: 0.291 AC: 4435 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3464

East Asian (EAS) AF: 0.496 AC: 2540 AN: 5116

South Asian (SAS) AF: 0.414 AC: 1987 AN: 4804

European-Finnish (FIN) AF: 0.398 AC: 4161 AN: 10454

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22323 AN: 67912

Other (OTH) AF: 0.298 AC: 627 AN: 2102

Alfa AF: 0.324 Hom.: 1358

Bravo AF: 0.302

Asia WGS AF: 0.413 AC: 1437 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	21
DANN	Benign	0.71
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1031282; hg19: chr8-137054657;