ENST00000502901.6:n.186-18268A>G

Variant names:

• chr8-136144207-A-G
• rs10505648
• ENST00000502901.6:n.186-18268A>G

Variant summary

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

The ENST00000502901.6(LINC02055):​n.186-18268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,610 control chromosomes in the GnomAD database, including 14,982 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 0.43 (14982 hom., cov: 31)
• Consequence: LINC02055 ENST00000502901.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502901.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02055	ENST00000502901.6	TSL:4	n.186-18268A>G		intron	N/A
	LINC02055	ENST00000523150.1	TSL:5	n.331-18268A>G		intron	N/A
	LINC02055	ENST00000648077.2		n.284-54023A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64455 AN: 151492 Hom.: 14983 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.425 AC: 64450 AN: 151610 Hom.: 14982 Cov.: 31 AF XY: 0.422 AC XY: 31284 AN XY: 74068

African (AFR) AF: 0.301 AC: 12451 AN: 41352

American (AMR) AF: 0.337 AC: 5127 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3466

East Asian (EAS) AF: 0.0933 AC: 476 AN: 5102

South Asian (SAS) AF: 0.294 AC: 1414 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5829 AN: 10538

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36041 AN: 67824

Other (OTH) AF: 0.429 AC: 900 AN: 2098

Alfa AF: 0.484 Hom.: 56588

Bravo AF: 0.403

Asia WGS AF: 0.211 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.60
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10505648; hg19: chr8-137156450;