rs138154934
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000052.7(ATP7A):āc.3475A>Gā(p.Thr1159Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000786 in 1,209,242 control chromosomes in the GnomAD database, including 2 homozygotes. There are 26 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1159I) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.3475A>G | p.Thr1159Ala | missense_variant | 17/23 | ENST00000341514.11 | |
ATP7A | NM_001282224.2 | c.3241A>G | p.Thr1081Ala | missense_variant | 16/22 | ||
ATP7A | NR_104109.2 | n.648A>G | non_coding_transcript_exon_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.3475A>G | p.Thr1159Ala | missense_variant | 17/23 | 1 | NM_000052.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000740 AC: 83AN: 112197Hom.: 2 Cov.: 23 AF XY: 0.000670 AC XY: 23AN XY: 34351
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183147Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67695
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097045Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 3AN XY: 362769
GnomAD4 genome ? AF: 0.000740 AC: 83AN: 112197Hom.: 2 Cov.: 23 AF XY: 0.000670 AC XY: 23AN XY: 34351
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2021 | Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar (ClinVar Variant ID# 465118; Landrum et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function - |
Menkes kinky-hair syndrome Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
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 | Invitae | Jan 17, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at