rs920455

Variant names:

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

Variant summary

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

The ENST00000518922.2(LINC02855):​n.122-3373T>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 ENST00000518922.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 5 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518922.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02855	NR_183453.1		n.199-3354T>C		intron	N/A
	LINC02855	NR_183454.1		n.199-3354T>C		intron	N/A
	LINC02855	NR_183455.1		n.48-3354T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAS2-AS1	ENST00000458107.3	TSL:5	n.251+7940A>G		intron	N/A
	LINC02855	ENST00000518922.2	TSL:3	n.122-3373T>C		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.753-19587A>G		intron	N/A

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

African (AFR) AF: 0.726 AC: 29929 AN: 41238

American (AMR) AF: 0.533 AC: 8126 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3470

East Asian (EAS) AF: 0.797 AC: 4059 AN: 5096

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4031 AN: 10496

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.324 AC: 22014 AN: 67860

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.363 Hom.: 8965

Bravo AF: 0.509

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		-0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs920455;

hg19: chr8-122700197;