8-136024974-C-G

Variant names:

• chr8-136024974-C-G
• rs2317356
• ENST00000650054.1:n.250+12787C>G

Variant summary

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

The ENST00000650054.1(LINC02055):​n.250+12787C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,040 control chromosomes in the GnomAD database, including 32,669 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 0.65 (32669 hom., cov: 33)
• Consequence: LINC02055 ENST00000650054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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	ENST00000650054.1	n.250+12787C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99414 AN: 151924 Hom.: 32632 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.654 AC: 99498 AN: 152040 Hom.: 32669 Cov.: 33 AF XY: 0.649 AC XY: 48262 AN XY: 74312

African (AFR) AF: 0.680 AC: 28184 AN: 41454

American (AMR) AF: 0.609 AC: 9297 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2519 AN: 5146

South Asian (SAS) AF: 0.588 AC: 2834 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6487 AN: 10568

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45417 AN: 68002

Other (OTH) AF: 0.669 AC: 1411 AN: 2108

Alfa AF: 0.527 Hom.: 1358

Bravo AF: 0.655

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.18
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2317356; hg19: chr8-137037217;