8-136972597-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000521034.1	n.304+10746A>G		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000649576.1	n.676+10746A>G		intron_variant, non_coding_transcript_variant

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;