X-78015836-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000052.7(ATP7A):c.2581C>T(p.Arg861Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,209,578 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R861H) has been classified as Likely benign.
Frequency
Consequence
NM_000052.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.2581C>T | p.Arg861Cys | missense_variant | 12/23 | ENST00000341514.11 | |
ATP7A | NM_001282224.2 | c.2347C>T | p.Arg783Cys | missense_variant | 11/22 | ||
ATP7A | NR_104109.2 | n.285-15564C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.2581C>T | p.Arg861Cys | missense_variant | 12/23 | 1 | NM_000052.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111966Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34158
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183362Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67832
GnomAD4 exome AF: 0.0000292 AC: 32AN: 1097612Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 13AN XY: 363010
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111966Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34158
ClinVar
Submissions by phenotype
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 | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at