rs782351352
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000052.7(ATP7A):āc.922A>Gā(p.Ile308Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,210,244 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 61 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000052.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.922A>G | p.Ile308Val | missense_variant | 4/23 | ENST00000341514.11 | NP_000043.4 | |
ATP7A | NM_001282224.2 | c.922A>G | p.Ile308Val | missense_variant | 4/22 | NP_001269153.1 | ||
ATP7A | NR_104109.2 | n.284+17783A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.922A>G | p.Ile308Val | missense_variant | 4/23 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.0000713 AC: 8AN: 112254Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34412
GnomAD3 exomes AF: 0.0000873 AC: 16AN: 183211Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67739
GnomAD4 exome AF: 0.000158 AC: 174AN: 1097990Hom.: 0 Cov.: 31 AF XY: 0.000165 AC XY: 60AN XY: 363398
GnomAD4 genome AF: 0.0000713 AC: 8AN: 112254Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34412
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | ATP7A: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 18, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Menkes kinky-hair syndrome;C0268353:Cutis laxa, X-linked;C1845359:X-linked distal spinal muscular atrophy type 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at