rs3870371

Variant names:

• chr8-121684892-C-A
• rs3870371
• ENST00000458107.3:n.251+4875C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-121684892-C-A
• chr8-121684892-C-G
• chr8-121684892-C-T

Variant summary

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

The ENST00000518922.2(LINC02855):​n.122-308G>T variant causes a intron 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 ENST00000518922.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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.199-289G>T		intron	N/A
	LINC02855	NR_183454.1		n.199-289G>T		intron	N/A
	LINC02855	NR_183455.1		n.48-289G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAS2-AS1	ENST00000458107.3	TSL:5	n.251+4875C>A		intron	N/A
	LINC02855	ENST00000518922.2	TSL:3	n.122-308G>T		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.753-22652C>A		intron	N/A

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

African (AFR) AF: 0.729 AC: 30135 AN: 41324

American (AMR) AF: 0.535 AC: 8147 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4116 AN: 5150

South Asian (SAS) AF: 0.381 AC: 1829 AN: 4796

European-Finnish (FIN) AF: 0.388 AC: 4031 AN: 10384

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.327 AC: 22172 AN: 67908

Other (OTH) AF: 0.491 AC: 1029 AN: 2094

Alfa AF: 0.355 Hom.: 8582

Bravo AF: 0.510

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.87

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: rs3870371;

hg19: chr8-122697132;