rs782094358
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_000052.7(ATP7A):c.2948C>T(p.Thr983Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,209,314 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 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.2948C>T | p.Thr983Met | missense_variant | 15/23 | ENST00000341514.11 | NP_000043.4 | |
ATP7A | NM_001282224.2 | c.2714C>T | p.Thr905Met | missense_variant | 14/22 | NP_001269153.1 | ||
ATP7A | NR_104109.2 | n.285-2119C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.2948C>T | p.Thr983Met | missense_variant | 15/23 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111665Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33863
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183332Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67814
GnomAD4 exome AF: 0.0000228 AC: 25AN: 1097649Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 6AN XY: 363031
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111665Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33863
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2021 | - - |
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 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at