rs279612

Variant names:

• chr8-121694051-A-G
• rs279612
• ENST00000458107.3:n.252-13493A>G

Variant summary

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

The ENST00000458107.3(HAS2-AS1):​n.252-13493A>G variant causes a intron 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: HAS2-AS1 ENST00000458107.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 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=-0.83).
• 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 rank	MANE	Protein	UniProt
LINC02855	NR_183453.1	n.198+1943T>C		intron_variant	Intron 2 of 4
LINC02855	NR_183454.1	n.198+1943T>C		intron_variant	Intron 2 of 4
LINC02855	NR_183455.1	n.47+3460T>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.252-13493A>G		intron_variant	Intron 2 of 2	5
LINC02855	ENST00000518922.2	n.121+3455T>C		intron_variant	Intron 1 of 3	3
HAS2-AS1	ENST00000648171.1	n.753-13493A>G		intron_variant	Intron 5 of 8

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

African (AFR) AF: 0.0146 AC: 609 AN: 41572

American (AMR) AF: 0.0387 AC: 592 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5172

South Asian (SAS) AF: 0.124 AC: 599 AN: 4824

European-Finnish (FIN) AF: 0.0687 AC: 728 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5845 AN: 68014

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0622 Hom.: 297

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs279612; hg19: chr8-122706291;