rs201225704
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_000052.7(ATP7A):āc.3449T>Cā(p.Ile1150Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000521 in 1,209,407 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1150L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000052.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.3449T>C | p.Ile1150Thr | missense_variant | 17/23 | ENST00000341514.11 | |
ATP7A | NM_001282224.2 | c.3215T>C | p.Ile1072Thr | missense_variant | 16/22 | ||
ATP7A | NR_104109.2 | n.622T>C | non_coding_transcript_exon_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.3449T>C | p.Ile1150Thr | missense_variant | 17/23 | 1 | NM_000052.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000161 AC: 18AN: 111950Hom.: 0 Cov.: 23 AF XY: 0.000176 AC XY: 6AN XY: 34114
GnomAD3 exomes AF: 0.0000873 AC: 16AN: 183317Hom.: 0 AF XY: 0.0000885 AC XY: 6AN XY: 67811
GnomAD4 exome AF: 0.0000410 AC: 45AN: 1097405Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 13AN XY: 362875
GnomAD4 genome ? AF: 0.000161 AC: 18AN: 112002Hom.: 0 Cov.: 23 AF XY: 0.000176 AC XY: 6AN XY: 34176
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 30, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | ATP7A: BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
ATP7A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Menkes kinky-hair syndrome;C0268353:Cutis laxa, X-linked;C1845359:X-linked distal spinal muscular atrophy type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at