rs920455

Variant names:

• chr8-121687957-A-G
• rs920455
• ENST00000458107.3:n.251+7940A>G

Variant summary

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

The NR_183453.1(LINC02855):​n.199-3354T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,526 control chromosomes in the GnomAD database, including 19,850 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 (19850 hom., cov: 32)
• Consequence: LINC02855 NR_183453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02855	NR_183453.1	n.199-3354T>C		intron_variant	Intron 2 of 4
LINC02855	NR_183454.1	n.199-3354T>C		intron_variant	Intron 2 of 4
LINC02855	NR_183455.1	n.48-3354T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAS2-AS1	ENST00000458107.3	n.251+7940A>G		intron_variant	Intron 2 of 2	5
HAS2-AS1	ENST00000648171.1	n.753-19587A>G		intron_variant	Intron 5 of 8
HAS2-AS1	ENST00000663147.1	n.729-19587A>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72459 AN: 151410 Hom.: 19797 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.479 AC: 72561 AN: 151526 Hom.: 19850 Cov.: 32 AF XY: 0.481 AC XY: 35607 AN XY: 74028

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.488

Alfa AF: 0.368 Hom.: 6405

Bravo AF: 0.509

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920455; hg19: chr8-122700197;