8-121878821-G-C

Variant names:

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

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>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,004 control chromosomes in the GnomAD database, including 122 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 0.026 (122 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0627 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>C		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.968+15812G>C		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.368-809G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0262 AC: 3972 AN: 151886 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00588

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000794

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0262 AC: 3990 AN: 152004 Hom.: 122 Cov.: 32 AF XY: 0.0265 AC XY: 1969 AN XY: 74306

African (AFR) AF: 0.0648 AC: 2684 AN: 41444

American (AMR) AF: 0.0418 AC: 638 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0598 AC: 309 AN: 5166

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4814

European-Finnish (FIN) AF: 0.00588 AC: 62 AN: 10548

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000794 AC: 54 AN: 67968

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.00114 Hom.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.65
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;