rs279612

chr8-121694051-A-G

Variant summary

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

The NR_183456.1(LINC02855):n.47+3460T>C 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 0.0594 in 152,268 control chromosomes in the GnomAD database, including 399 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 0.059 (399 hom., cov: 32)
• Consequence: LINC02855 NR_183456.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

LINC02855 (HGNC:54392): (long intergenic non-protein coding RNA 2855)

HAS2-AS1 (HGNC:34340): (HAS2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02855	NR_183456.1	n.47+3460T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02855	ENST00000663221.1	n.52+3460T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9054 AN: 152150 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0594 AC: 9052 AN: 152268 Hom.: 399 Cov.: 32 AF XY: 0.0598 AC XY: 4454 AN XY: 74452

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0596

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0745 Hom.: 107

Bravo AF: 0.0535

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.9
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs279612; hg19: chr8-122706291;