8-121796367-C-A

Variant names:

• chr8-121796367-C-A
• rs7846389
• ENST00000647560.2:n.311-83263C>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.311-83263C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,916 control chromosomes in the GnomAD database, including 23,396 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 0.54 (23396 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000647560.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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

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	ENST00000647560.2		n.311-83263C>A		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.885-66559C>A		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.284-66559C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82742 AN: 151798 Hom.: 23393 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.545 AC: 82774 AN: 151916 Hom.: 23396 Cov.: 32 AF XY: 0.548 AC XY: 40658 AN XY: 74216

African (AFR) AF: 0.408 AC: 16898 AN: 41396

American (AMR) AF: 0.491 AC: 7495 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2124 AN: 5164

South Asian (SAS) AF: 0.588 AC: 2823 AN: 4798

European-Finnish (FIN) AF: 0.664 AC: 6987 AN: 10526

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42554 AN: 67968

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.584 Hom.: 12279

Bravo AF: 0.522

Asia WGS AF: 0.494 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.99
DANN	Benign	0.51
PhyloP100		-1.1

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: rs7846389;

hg19: chr8-122808607;