rs17647890

Variant names:

• chr8-136742324-G-A
• rs17647890
• ENST00000517345.6:n.85-47511G>A

Variant summary

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

The ENST00000517345.6(LINC02055):​n.85-47511G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,642 control chromosomes in the GnomAD database, including 5,782 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 0.26 (5782 hom., cov: 32)
• Consequence: LINC02055 ENST00000517345.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.292-47511G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000517345.6	n.85-47511G>A		intron_variant	Intron 1 of 3	3
LINC02055	ENST00000524346.6	n.319-47511G>A		intron_variant	Intron 2 of 5	3
LINC02055	ENST00000649576.1	n.319-47511G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39680 AN: 151526 Hom.: 5778 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.262 AC: 39701 AN: 151642 Hom.: 5782 Cov.: 32 AF XY: 0.264 AC XY: 19563 AN XY: 74096

African (AFR) AF: 0.199 AC: 8253 AN: 41476

American (AMR) AF: 0.274 AC: 4163 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1083 AN: 4748

European-Finnish (FIN) AF: 0.333 AC: 3508 AN: 10534

Middle Eastern (MID) AF: 0.214 AC: 62 AN: 290

European-Non Finnish (NFE) AF: 0.296 AC: 20051 AN: 67734

Other (OTH) AF: 0.242 AC: 507 AN: 2094

Alfa AF: 0.276 Hom.: 2916

Bravo AF: 0.256

Asia WGS AF: 0.225 AC: 781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.53
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs17647890; hg19: chr8-137754567;