rs2317356

Positions:

• chr8-136024974-C-G
• chr8-136024974-C-T

Variant summary

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

The ENST00000650054.1(LINC02055):​n.250+12787C>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 0.654 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

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=-0.91).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02055	ENST00000650054.1	n.250+12787C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.669

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317356; hg19: chr8-137037217;