rs1557239138
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_000052.7(ATP7A):āc.4422A>Gā(p.Leu1474=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,097,906 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L1474L) has been classified as Likely benign.
Frequency
Consequence
NM_000052.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.4422A>G | p.Leu1474= | synonymous_variant | 23/23 | ENST00000341514.11 | |
ATP7A | NM_001282224.2 | c.4188A>G | p.Leu1396= | synonymous_variant | 22/22 | ||
ATP7A | NR_104109.2 | n.1595A>G | non_coding_transcript_exon_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.4422A>G | p.Leu1474= | synonymous_variant | 23/23 | 1 | NM_000052.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111284Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33464
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183294Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67802
GnomAD4 exome AF: 0.0000173 AC: 19AN: 1097906Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 363270
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000899 AC: 1AN: 111284Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33464
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 01, 2020 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at