rs12680546

Variant names:

• chr8-135859496-A-G
• rs12680546
• ENST00000648045.1:n.128A>G

Variant summary

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

The ENST00000648045.1(LINC02055):​n.128A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,178 control chromosomes in the GnomAD database, including 3,762 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 0.20 (3762 hom., cov: 32)
• Consequence: LINC02055 ENST00000648045.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.277 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	ENST00000648045.1	n.128A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02055	ENST00000650217.1	n.128A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31199 AN: 152060 Hom.: 3765 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.205 AC: 31191 AN: 152178 Hom.: 3762 Cov.: 32 AF XY: 0.200 AC XY: 14860 AN XY: 74378

African (AFR) AF: 0.0813 AC: 3375 AN: 41534

American (AMR) AF: 0.181 AC: 2766 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3470

East Asian (EAS) AF: 0.101 AC: 523 AN: 5172

South Asian (SAS) AF: 0.173 AC: 832 AN: 4810

European-Finnish (FIN) AF: 0.216 AC: 2289 AN: 10594

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19032 AN: 68006

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.260 Hom.: 25661

Bravo AF: 0.199

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12680546; hg19: chr8-136871739;