rs764551529
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000053.4(ATP7B):c.1185C>T(p.Ala395Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A395A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
ATP7B
NM_000053.4 synonymous
NM_000053.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.708
Publications
2 publications found
Genes affected
ATP7B (HGNC:870): (ATPase copper transporting beta) This gene is a member of the P-type cation transport ATPase family and encodes a protein with several membrane-spanning domains, an ATPase consensus sequence, a hinge domain, a phosphorylation site, and at least 2 putative copper-binding sites. This protein is a monomer, and functions as a copper-transporting ATPase which exports copper out of the cells, such as the efflux of hepatic copper into the bile. Alternate transcriptional splice variants, encoding different isoforms with distinct cellular localizations, have been characterized. Mutations in this gene have been associated with Wilson disease which is characterized by copper accumulation. [provided by RefSeq, Dec 2019]
ATP7B Gene-Disease associations (from GenCC):
- Wilson diseaseInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 13-51974035-G-A is Benign according to our data. Variant chr13-51974035-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 526666.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.708 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000053.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATP7B | NM_000053.4 | MANE Select | c.1185C>T | p.Ala395Ala | synonymous | Exon 2 of 21 | NP_000044.2 | ||
| ATP7B | NM_001406511.1 | c.1185C>T | p.Ala395Ala | synonymous | Exon 3 of 22 | NP_001393440.1 | |||
| ATP7B | NM_001406512.1 | c.1185C>T | p.Ala395Ala | synonymous | Exon 3 of 22 | NP_001393441.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATP7B | ENST00000242839.10 | TSL:1 MANE Select | c.1185C>T | p.Ala395Ala | synonymous | Exon 2 of 21 | ENSP00000242839.5 | ||
| ATP7B | ENST00000634844.1 | TSL:1 | c.1185C>T | p.Ala395Ala | synonymous | Exon 2 of 21 | ENSP00000489398.1 | ||
| ATP7B | ENST00000418097.7 | TSL:1 | c.1185C>T | p.Ala395Ala | synonymous | Exon 2 of 20 | ENSP00000393343.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000200 AC: 5AN: 249552 AF XY: 0.0000222 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
249552
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1461892
Hom.:
Cov.:
34
AF XY:
AC XY:
2
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
2
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1112010
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.454
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
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Bravo
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EpiCase
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ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
3
Wilson disease (3)
Computational 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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