8-136582281-A-G

Variant names:

• chr8-136582281-A-G
• rs305283
• ENST00000517345.6:n.84+45222A>G

Variant summary

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

The ENST00000517345.6(LINC02055):​n.84+45222A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 151,922 control chromosomes in the GnomAD database, including 62,704 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 0.91 (62704 hom., cov: 31)
• Consequence: LINC02055 ENST00000517345.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517345.6. 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
	LINC02055	NR_147196.1		n.291+45222A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000517345.6	TSL:3	n.84+45222A>G		intron	N/A
	LINC02055	ENST00000520060.3	TSL:4	n.344+45222A>G		intron	N/A
	LINC02055	ENST00000523232.3	TSL:4	n.743-16490A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.908 AC: 137781 AN: 151806 Hom.: 62671 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.908 AC: 137871 AN: 151922 Hom.: 62704 Cov.: 31 AF XY: 0.904 AC XY: 67165 AN XY: 74262

African (AFR) AF: 0.919 AC: 38139 AN: 41508

American (AMR) AF: 0.845 AC: 12898 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3270 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3948 AN: 5160

South Asian (SAS) AF: 0.917 AC: 4429 AN: 4828

European-Finnish (FIN) AF: 0.921 AC: 9739 AN: 10580

Middle Eastern (MID) AF: 0.894 AC: 261 AN: 292

European-Non Finnish (NFE) AF: 0.920 AC: 62396 AN: 67802

Other (OTH) AF: 0.906 AC: 1909 AN: 2106

Alfa AF: 0.906 Hom.: 3277

Bravo AF: 0.901

Asia WGS AF: 0.828 AC: 2869 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs305283; hg19: chr8-137594524;