chrX-77910848-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000052.7(ATP7A):c.-22+13T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 112,335 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000052.7 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.-22+13T>G | intron_variant | Intron 1 of 22 | ENST00000341514.11 | NP_000043.4 | ||
ATP7A | NM_001282224.2 | c.-22+13T>G | intron_variant | Intron 1 of 21 | NP_001269153.1 | |||
ATP7A | NR_104109.2 | n.143+13T>G | intron_variant | Intron 1 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112335Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34497
GnomAD4 exome Cov.: 0
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112335Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34497
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at