rs12680546

Positions:

• chr8-135859496-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000648045.1	n.128A>G		non_coding_transcript_exon_variant	1/3
LINC02055	ENST00000650217.1	n.128A>G		non_coding_transcript_exon_variant	1/4

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

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.233

Alfa AF: 0.272 Hom.: 13499

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12680546; hg19: chr8-136871739;