8-136972597-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521034.1(LINC02055):​n.304+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 ENST00000521034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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 (AMR) allele frequency at 95% confidence interval = 0.0718 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	ENST00000521034.1	n.304+10746A>G		intron_variant	Intron 3 of 3	5
LINC02055	ENST00000649576.1	n.676+10746A>G		intron_variant	Intron 6 of 8

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

Gnomad4 AFR AF: 0.0392

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0675

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.0272

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.0383 Hom.: 190

Bravo AF: 0.0489

Asia WGS AF: 0.0960 AC: 331 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	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1909486; hg19: chr8-137984840;