8-121878821-G-T

Variant names:

• chr8-121878821-G-T
• rs6981419
• ENST00000647560.2:n.311-809G>T

Variant summary

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

The ENST00000647560.2(HAS2-AS1):​n.311-809G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,978 control chromosomes in the GnomAD database, including 2,520 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 0.16 (2520 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000647560.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647560.2. 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	ENST00000647560.2		n.311-809G>T		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.968+15812G>T		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.368-809G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24253 AN: 151860 Hom.: 2510 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.160 AC: 24291 AN: 151978 Hom.: 2520 Cov.: 32 AF XY: 0.165 AC XY: 12288 AN XY: 74286

African (AFR) AF: 0.157 AC: 6526 AN: 41444

American (AMR) AF: 0.248 AC: 3791 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2854 AN: 5164

South Asian (SAS) AF: 0.187 AC: 902 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1161 AN: 10538

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7902 AN: 67962

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.0436 Hom.: 35

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6981419; hg19: chr8-122891060;