Variant 3-10328802-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001001331.4(ATP2B2):c.*12C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,596,812 control chromosomes in the GnomAD database, including 75,076 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 9507 hom., cov: 29)

Exomes 𝑓: 0.29 ( 65569 hom. )

Consequence

ATP2B2
NM_001001331.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.256

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]

ATP2B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 3-10328802-G-C is Benign according to our data. Variant chr3-10328802-G-C is described in ClinVar as [Benign]. Clinvar id is 1279072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP2B2	NM_001001331.4 linkuse as main transcript	c.*12C>G		3_prime_UTR_variant	23/23	ENST00000360273.7	NP_001001331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP2B2	ENST00000360273.7 linkuse as main transcript	c.*12C>G		3_prime_UTR_variant	23/23	5	NM_001001331.4	ENSP00000353414		Q01814-1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51074

AN:

151356

Hom.:

9493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.441

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.587

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.311

GnomAD3 exomes

AF:

0.344

AC:

84436

AN:

245646

Hom.:

16151

AF XY:

0.343

AC XY:

45426

AN XY:

132502

show subpopulations

Gnomad AFR exome

AF:

0.445

Gnomad AMR exome

AF:

0.398

Gnomad ASJ exome

AF:

0.248

Gnomad EAS exome

AF:

0.590

Gnomad SAS exome

AF:

0.472

Gnomad FIN exome

AF:

0.338

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.287

AC:

414710

AN:

1445338

Hom.:

65569

Cov.:

AF XY:

0.291

AC XY:

208362

AN XY:

715790

show subpopulations

Gnomad4 AFR exome

AF:

0.449

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.243

Gnomad4 EAS exome

AF:

0.624

Gnomad4 SAS exome

AF:

0.469

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.301

GnomAD4 genome

AF:

0.338

AC:

51139

AN:

151474

Hom.:

9507

Cov.:

AF XY:

0.346

AC XY:

25611

AN XY:

73994

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.587

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.311

Alfa

AF:

0.290

Hom.:

1305

Bravo

AF:

0.343

Asia WGS

AF:

0.527

AC:

1828

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

5.9

DANN

Benign

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over