rs186012808

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_004320.6(ATP2A1):​c.2536G>A​(p.Ala846Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000413 in 1,614,072 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00040 ( 3 hom. )

Consequence

ATP2A1
NM_004320.6 missense

Scores

1
9
9

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: 4.79
Variant links:
Genes affected
ATP2A1 (HGNC:811): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen, and is involved in muscular excitation and contraction. Mutations in this gene cause some autosomal recessive forms of Brody disease, characterized by increasing impairment of muscular relaxation during exercise. Alternative splicing results in three transcript variants encoding different isoforms. [provided by RefSeq, Oct 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0117560625).
BP6
Variant 16-28902591-G-A is Benign according to our data. Variant chr16-28902591-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 431853.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=2}.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000404 (590/1461846) while in subpopulation AFR AF= 0.00108 (36/33480). AF 95% confidence interval is 0.000798. There are 3 homozygotes in gnomad4_exome. There are 314 alleles in male gnomad4_exome subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATP2A1NM_004320.6 linkuse as main transcriptc.2536G>A p.Ala846Thr missense_variant 18/23 ENST00000395503.9 NP_004311.1 O14983-2Q7Z675
ATP2A1NM_173201.5 linkuse as main transcriptc.2536G>A p.Ala846Thr missense_variant 18/22 NP_775293.1 O14983-1Q7Z675
ATP2A1NM_001286075.2 linkuse as main transcriptc.2161G>A p.Ala721Thr missense_variant 16/21 NP_001273004.1 O14983-3Q7Z675

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATP2A1ENST00000395503.9 linkuse as main transcriptc.2536G>A p.Ala846Thr missense_variant 18/231 NM_004320.6 ENSP00000378879.5 O14983-2
ATP2A1ENST00000357084.7 linkuse as main transcriptc.2536G>A p.Ala846Thr missense_variant 18/222 ENSP00000349595.3 O14983-1
ATP2A1ENST00000536376.5 linkuse as main transcriptc.2161G>A p.Ala721Thr missense_variant 16/212 ENSP00000443101.1 O14983-3

Frequencies

GnomAD3 genomes
AF:
0.000500
AC:
76
AN:
152108
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000628
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.0118
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000729
AC:
183
AN:
251164
Hom.:
2
AF XY:
0.000685
AC XY:
93
AN XY:
135786
show subpopulations
Gnomad AFR exome
AF:
0.000677
Gnomad AMR exome
AF:
0.0000868
Gnomad ASJ exome
AF:
0.0155
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000404
AC:
590
AN:
1461846
Hom.:
3
Cov.:
34
AF XY:
0.000432
AC XY:
314
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.0158
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000612
Gnomad4 OTH exome
AF:
0.00113
GnomAD4 genome
AF:
0.000499
AC:
76
AN:
152226
Hom.:
0
Cov.:
31
AF XY:
0.000470
AC XY:
35
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.000626
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.0118
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.00121
Hom.:
1
Bravo
AF:
0.000570
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000455
AC:
2
ESP6500EA
AF:
0.000814
AC:
7
ExAC
AF:
0.000486
AC:
59
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.000436
EpiControl
AF:
0.000237

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Brody myopathy Uncertain:1Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 26, 2024- -
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingGeneDxNov 15, 2019- -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsDec 04, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.066
T
BayesDel_noAF
Uncertain
0.060
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.62
D;.;.
Eigen
Benign
-0.0014
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.91
D;D;D
M_CAP
Pathogenic
0.36
D
MetaRNN
Benign
0.012
T;T;T
MetaSVM
Uncertain
0.50
D
MutationAssessor
Uncertain
2.1
M;M;.
PrimateAI
Uncertain
0.57
T
PROVEAN
Benign
-1.9
N;N;N
REVEL
Uncertain
0.56
Sift
Benign
0.26
T;T;T
Sift4G
Benign
0.10
T;T;T
Polyphen
0.056
B;B;.
Vest4
0.48
MVP
0.92
MPC
0.87
ClinPred
0.027
T
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.54
gMVP
0.70

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: rs186012808; hg19: chr16-28913912; COSMIC: COSV62870326; COSMIC: COSV62870326; API