rs12579003

Variant names:

• chr12-89768083-C-T
• rs12579003
• ENST00000651272.1:n.360-32878C>T

Variant summary

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

The ENST00000651272.1(ATP2B1-AS1):​n.360-32878C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,132 control chromosomes in the GnomAD database, including 798 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 0.086 (798 hom., cov: 32)
• Consequence: ATP2B1-AS1 ENST00000651272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 5 publications found

Genes affected

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

ENSG00000296746 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651272.1. 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	ENST00000651272.1		n.360-32878C>T		intron	N/A
	ENSG00000296746	ENST00000741520.1		n.175+15628G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13033 AN: 152014 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0857 AC: 13042 AN: 152132 Hom.: 798 Cov.: 32 AF XY: 0.0925 AC XY: 6878 AN XY: 74356

African (AFR) AF: 0.0350 AC: 1453 AN: 41536

American (AMR) AF: 0.169 AC: 2582 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.145 AC: 751 AN: 5162

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4822

European-Finnish (FIN) AF: 0.174 AC: 1834 AN: 10558

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0843 AC: 5735 AN: 68004

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0808 Hom.: 1009

Bravo AF: 0.0861

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.42
PhyloP100		-0.49

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: rs12579003;

hg19: chr12-90161860;