8-121897448-A-G

Variant names:

• chr8-121897448-A-G
• rs956225
• ENST00000523550.1:n.315-5991A>G

Variant summary

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

The ENST00000523550.1(HAS2-AS1):​n.315-5991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,150 control chromosomes in the GnomAD database, including 1,325 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 0.12 (1325 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000523550.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523550.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAS2-AS1	ENST00000523550.1	TSL:3	n.315-5991A>G		intron	N/A
	HAS2-AS1	ENST00000647560.2		n.446+17683A>G		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.969-5991A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18108 AN: 152032 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.119 AC: 18104 AN: 152150 Hom.: 1325 Cov.: 32 AF XY: 0.122 AC XY: 9107 AN XY: 74382

African (AFR) AF: 0.0286 AC: 1189 AN: 41546

American (AMR) AF: 0.114 AC: 1751 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3468

East Asian (EAS) AF: 0.131 AC: 676 AN: 5174

South Asian (SAS) AF: 0.120 AC: 580 AN: 4828

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10556

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10583 AN: 67964

Other (OTH) AF: 0.132 AC: 278 AN: 2114

Alfa AF: 0.140 Hom.: 5564

Bravo AF: 0.109

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs956225; hg19: chr8-122909687;