rs10089677

Variant names:

• chr8-121648008-G-A
• rs10089677
• ENST00000648171.1:n.752+3617G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-121648008-G-A
• chr8-121648008-G-C

Variant summary

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

The ENST00000648171.1(HAS2-AS1):​n.752+3617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,020 control chromosomes in the GnomAD database, including 29,929 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 0.61 (29929 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000648171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648171.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAS2-AS1	ENST00000648171.1		n.752+3617G>A		intron	N/A
	HAS2-AS1	ENST00000663147.1		n.728+3617G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92722 AN: 151902 Hom.: 29881 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.611 AC: 92827 AN: 152020 Hom.: 29929 Cov.: 32 AF XY: 0.611 AC XY: 45431 AN XY: 74300

African (AFR) AF: 0.804 AC: 33377 AN: 41498

American (AMR) AF: 0.627 AC: 9573 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3468

East Asian (EAS) AF: 0.863 AC: 4454 AN: 5162

South Asian (SAS) AF: 0.510 AC: 2455 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5672 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33536 AN: 67968

Other (OTH) AF: 0.613 AC: 1295 AN: 2112

Alfa AF: 0.533 Hom.: 35484

Bravo AF: 0.631

Asia WGS AF: 0.723 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		0.37

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: rs10089677;

hg19: chr8-122660248;