8-121733090-G-A

Variant names:

• chr8-121733090-G-A
• rs10106208
• ENST00000647560.2:n.310+25415G>A

Variant summary

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

The ENST00000647560.2(HAS2-AS1):​n.310+25415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,192 control chromosomes in the GnomAD database, including 431 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 0.066 (431 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000647560.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0955 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.310+25415G>A		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.884+25415G>A		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.283+25415G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10006 AN: 152074 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0657 AC: 10005 AN: 152192 Hom.: 431 Cov.: 32 AF XY: 0.0639 AC XY: 4754 AN XY: 74414

African (AFR) AF: 0.0186 AC: 774 AN: 41536

American (AMR) AF: 0.0547 AC: 837 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10564

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6626 AN: 68010

Other (OTH) AF: 0.0646 AC: 136 AN: 2104

Alfa AF: 0.0882 Hom.: 356

Bravo AF: 0.0604

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10106208; hg19: chr8-122745330;