rs369766004
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_014861.4(ATP2C2):c.270C>A(p.Gly90Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G90G) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000079 ( 0 hom. )
Consequence
ATP2C2
NM_014861.4 synonymous
NM_014861.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.12
Publications
0 publications found
Genes affected
ATP2C2 (HGNC:29103): (ATPase secretory pathway Ca2+ transporting 2) Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; cellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP7
Synonymous conserved (PhyloP=3.12 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ATP2C2 | NM_014861.4 | c.270C>A | p.Gly90Gly | synonymous_variant | Exon 3 of 27 | ENST00000262429.9 | NP_055676.3 | |
| ATP2C2 | NM_001286527.3 | c.270C>A | p.Gly90Gly | synonymous_variant | Exon 3 of 28 | NP_001273456.2 | ||
| ATP2C2 | XM_011523486.3 | c.201C>A | p.Gly67Gly | synonymous_variant | Exon 3 of 28 | XP_011521788.1 | ||
| ATP2C2 | XM_047434994.1 | c.201C>A | p.Gly67Gly | synonymous_variant | Exon 3 of 27 | XP_047290950.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ATP2C2 | ENST00000262429.9 | c.270C>A | p.Gly90Gly | synonymous_variant | Exon 3 of 27 | 1 | NM_014861.4 | ENSP00000262429.4 | ||
| ATP2C2 | ENST00000416219.7 | c.270C>A | p.Gly90Gly | synonymous_variant | Exon 3 of 28 | 1 | ENSP00000397925.2 | |||
| ATP2C2 | ENST00000565631.5 | n.761C>A | non_coding_transcript_exon_variant | Exon 1 of 25 | 2 | |||||
| ATP2C2 | ENST00000569207.5 | n.-34C>A | upstream_gene_variant | 5 | ENSP00000456595.1 |
Frequencies
GnomAD3 genomes 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
5
AN:
152120
Hom.:
Cov.:
32
Gnomad AFR
AF:
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000241 AC: 6AN: 249406 AF XY: 0.0000296 show subpopulations
GnomAD2 exomes
AF:
AC:
6
AN:
249406
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727222 show subpopulations
GnomAD4 exome
AF:
AC:
116
AN:
1461854
Hom.:
Cov.:
31
AF XY:
AC XY:
49
AN XY:
727222
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
AC:
0
AN:
53406
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
110
AN:
1111996
Other (OTH)
AF:
AC:
6
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.453
Heterozygous variant carriers
0
7
14
21
28
35
0.00
0.20
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0.80
0.95
Allele balance
GnomAD4 genome 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74282 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
152120
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
74282
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41410
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10610
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
5
AN:
68028
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.445
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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