rs782237314
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_000052.7(ATP7A):āc.844A>Gā(p.Ile282Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000479 in 1,210,331 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000052.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.844A>G | p.Ile282Val | missense_variant | 4/23 | ENST00000341514.11 | NP_000043.4 | |
ATP7A | NM_001282224.2 | c.844A>G | p.Ile282Val | missense_variant | 4/22 | NP_001269153.1 | ||
ATP7A | NR_104109.2 | n.284+17705A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.844A>G | p.Ile282Val | missense_variant | 4/23 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112224Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34382
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 183020Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67626
GnomAD4 exome AF: 0.0000501 AC: 55AN: 1098107Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 16AN XY: 363517
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112224Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34382
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | ATP7A: BP4 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 05, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 29, 2023 | The c.844A>G (p.I282V) alteration is located in exon 4 (coding exon 3) of the ATP7A gene. This alteration results from a A to G substitution at nucleotide position 844, causing the isoleucine (I) at amino acid position 282 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at