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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000650054.1	n.250+30227G>A		intron_variant	Intron 2 of 5

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

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.298

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031282; hg19: chr8-137054657;