rs3870371

chr8-121684892-C-Achr8-121684892-C-Gchr8-121684892-C-T

Variant summary

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

The NR_183456.1(LINC02855):n.48-4451G>T 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 0.482 in 151,566 control chromosomes in the GnomAD database, including 20,121 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 0.48 (20121 hom., cov: 31)
• Consequence: LINC02855 NR_183456.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02855	NR_183456.1	n.48-4451G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02855	ENST00000663221.1	n.53-289G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72905 AN: 151458 Hom.: 20066 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.482 AC: 73009 AN: 151566 Hom.: 20121 Cov.: 31 AF XY: 0.484 AC XY: 35819 AN XY: 74008

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.491

Alfa AF: 0.357 Hom.: 6016

Bravo AF: 0.510

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3870371; hg19: chr8-122697132;