8-136972597-A-G

Variant names:

• chr8-136972597-A-G
• rs1909486
• ENST00000521034.1:n.304+10746A>G

Variant summary

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

The ENST00000649576.1(LINC02055):​n.676+10746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,186 control chromosomes in the GnomAD database, including 162 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 0.043 (162 hom., cov: 33)
• Consequence: LINC02055 ENST00000649576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649576.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000521034.1	TSL:5	n.304+10746A>G		intron	N/A
	LINC02055	ENST00000649576.1		n.676+10746A>G		intron	N/A
	LINC02055	ENST00000837562.1		n.264+10746A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6575 AN: 152068 Hom.: 157 Cov.: 33

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0433 AC: 6589 AN: 152186 Hom.: 162 Cov.: 33 AF XY: 0.0432 AC XY: 3214 AN XY: 74408

African (AFR) AF: 0.0392 AC: 1627 AN: 41552

American (AMR) AF: 0.0754 AC: 1150 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3470

East Asian (EAS) AF: 0.0675 AC: 349 AN: 5172

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4828

European-Finnish (FIN) AF: 0.0272 AC: 288 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2634 AN: 68014

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0410 Hom.: 285

Bravo AF: 0.0489

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.82
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1909486; hg19: chr8-137984840;