rs1062472
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000052.7(ATP7A):c.*1960T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 110,589 control chromosomes in the GnomAD database, including 10,795 homozygotes. There are 14,325 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000052.7 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.*1960T>C | 3_prime_UTR_variant | 23/23 | ENST00000341514.11 | ||
ATP7A | NM_001282224.2 | c.*1960T>C | 3_prime_UTR_variant | 22/22 | |||
ATP7A | NR_104109.2 | n.3636T>C | non_coding_transcript_exon_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.*1960T>C | 3_prime_UTR_variant | 23/23 | 1 | NM_000052.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.449 AC: 49524AN: 110239Hom.: 10779 Cov.: 22 AF XY: 0.438 AC XY: 14244AN XY: 32487
GnomAD4 exome AF: 0.272 AC: 81AN: 298Hom.: 7 Cov.: 0 AF XY: 0.222 AC XY: 28AN XY: 126
GnomAD4 genome ? AF: 0.450 AC: 49593AN: 110291Hom.: 10788 Cov.: 22 AF XY: 0.439 AC XY: 14297AN XY: 32549
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at