8-136582281-A-G

Position:

• chr8-136582281-A-G

Variant summary

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

The NR_147196.1(LINC02055):​n.291+45222A>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 0.908 in 151,922 control chromosomes in the GnomAD database, including 62,704 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 0.91 (62704 hom., cov: 31)
• Consequence: LINC02055 NR_147196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02055	NR_147196.1	n.291+45222A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000650445.2	n.918+45222A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.908 AC: 137781 AN: 151806 Hom.: 62671 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.908 AC: 137871 AN: 151922 Hom.: 62704 Cov.: 31 AF XY: 0.904 AC XY: 67165 AN XY: 74262

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.906

Alfa AF: 0.906 Hom.: 2959

Bravo AF: 0.901

Asia WGS AF: 0.828 AC: 2869 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305283; hg19: chr8-137594524;