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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984543	XR_007063399.1	n.171-32878C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2B1-AS1	ENST00000651272.1	n.360-32878C>T		intron_variant	Intron 2 of 6
ENSG00000296746	ENST00000741520.1	n.175+15628G>A		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs12579003; hg19: chr12-90161860;