rs2278556

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001001331.4(ATP2B2):​c.1660-296C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,144 control chromosomes in the GnomAD database, including 10,243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 10243 hom., cov: 33)

Consequence

ATP2B2
NM_001001331.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.720
Variant links:
Genes affected
ATP2B2 (HGNC:815): (ATPase plasma membrane Ca2+ transporting 2) 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 2. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 3-10360419-G-A is Benign according to our data. Variant chr3-10360419-G-A is described in ClinVar as [Benign]. Clinvar id is 1296800.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATP2B2NM_001001331.4 linkuse as main transcriptc.1660-296C>T intron_variant ENST00000360273.7 NP_001001331.1 Q01814-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATP2B2ENST00000360273.7 linkuse as main transcriptc.1660-296C>T intron_variant 5 NM_001001331.4 ENSP00000353414.2 Q01814-1

Frequencies

GnomAD3 genomes
AF:
0.347
AC:
52788
AN:
152026
Hom.:
10244
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.179
Gnomad AMI
AF:
0.488
Gnomad AMR
AF:
0.495
Gnomad ASJ
AF:
0.303
Gnomad EAS
AF:
0.543
Gnomad SAS
AF:
0.522
Gnomad FIN
AF:
0.394
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.381
Gnomad OTH
AF:
0.364
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.347
AC:
52817
AN:
152144
Hom.:
10243
Cov.:
33
AF XY:
0.354
AC XY:
26361
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.180
Gnomad4 AMR
AF:
0.495
Gnomad4 ASJ
AF:
0.303
Gnomad4 EAS
AF:
0.544
Gnomad4 SAS
AF:
0.521
Gnomad4 FIN
AF:
0.394
Gnomad4 NFE
AF:
0.381
Gnomad4 OTH
AF:
0.362
Alfa
AF:
0.381
Hom.:
22511
Bravo
AF:
0.343
Asia WGS
AF:
0.534
AC:
1855
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
16
DANN
Benign
0.75

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2278556; hg19: chr3-10402103; API