rs2070759

chr12-89623959-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366521.1(ATP2B1):c.1344+224C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,964 control chromosomes in the GnomAD database, including 19,195 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 0.49 (19195 hom., cov: 32)
• Consequence: ATP2B1 NM_001366521.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

ATP2B1 (HGNC:814): (ATPase plasma membrane Ca2+ transporting 1) The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 1. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP2B1	NM_001366521.1	c.1344+224C>A		intron_variant		ENST00000428670.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP2B1	ENST00000428670.8	c.1344+224C>A		intron_variant		5	NM_001366521.1	P1
ATP2B1	ENST00000359142.8	c.1344+224C>A		intron_variant		5
ATP2B1	ENST00000551310.2	c.1344+224C>A		intron_variant		3
ATP2B1	ENST00000705822.1	c.1344+224C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74328 AN: 151846 Hom.: 19180 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.489 AC: 74361 AN: 151964 Hom.: 19195 Cov.: 32 AF XY: 0.493 AC XY: 36597 AN XY: 74252

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.523

Alfa AF: 0.531 Hom.: 32533

Bravo AF: 0.483

Asia WGS AF: 0.536 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070759; hg19: chr12-90017736;