12-89912002-A-G

Variant names:

• chr12-89912002-A-G
• rs7965584
• ENST00000547370.5:n.228-9065A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000547370.5(ATP2B1-AS1):​n.228-9065A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0041 (3 hom., cov: 18)
• Consequence: ATP2B1-AS1 ENST00000547370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 23 publications found

Genes affected

ATP2B1-AS1 (HGNC:27883): (ATP2B1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547370.5. 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
	ATP2B1-AS1	ENST00000547370.5	TSL:4	n.228-9065A>G		intron	N/A
	ATP2B1-AS1	ENST00000651272.1		n.402-9065A>G		intron	N/A
	ATP2B1-AS1	ENST00000716130.1		n.309-9065A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00406 AC: 480 AN: 118212 Hom.: 3 Cov.: 18

Gnomad AFR AF: 0.00151

Gnomad AMI AF: 0.00159

Gnomad AMR AF: 0.00297

Gnomad ASJ AF: 0.00110

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.000587

Gnomad MID AF: 0.0115

Gnomad NFE AF: 0.00569

Gnomad OTH AF: 0.00743

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

GnomAD4 genome AF: 0.00406 AC: 480 AN: 118304 Hom.: 3 Cov.: 18 AF XY: 0.00435 AC XY: 249 AN XY: 57260

African (AFR) AF: 0.00150 AC: 55 AN: 36614

American (AMR) AF: 0.00296 AC: 35 AN: 11820

Ashkenazi Jewish (ASJ) AF: 0.00110 AC: 3 AN: 2736

East Asian (EAS) AF: 0.0107 AC: 42 AN: 3932

South Asian (SAS) AF: 0.0107 AC: 39 AN: 3644

European-Finnish (FIN) AF: 0.000587 AC: 4 AN: 6818

Middle Eastern (MID) AF: 0.0124 AC: 3 AN: 242

European-Non Finnish (NFE) AF: 0.00569 AC: 286 AN: 50242

Other (OTH) AF: 0.00737 AC: 12 AN: 1628

Alfa AF: 0.238 Hom.: 7438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7965584; hg19: chr12-90305779;