rs368261204
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The ENST00000341514.11(ATP7A):c.2490C>T(p.Ile830=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000037 in 1,079,735 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
ENST00000341514.11 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP7A | NM_000052.7 | c.2490C>T | p.Ile830= | synonymous_variant | 11/23 | ENST00000341514.11 | NP_000043.4 | |
ATP7A | NM_001282224.2 | c.2256C>T | p.Ile752= | synonymous_variant | 10/22 | NP_001269153.1 | ||
ATP7A | NR_104109.2 | n.285-16655C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP7A | ENST00000341514.11 | c.2490C>T | p.Ile830= | synonymous_variant | 11/23 | 1 | NM_000052.7 | ENSP00000345728 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000553 AC: 1AN: 180918Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65522
GnomAD4 exome AF: 0.00000370 AC: 4AN: 1079735Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 346395
GnomAD4 genome Cov.: 23
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 | Labcorp Genetics (formerly Invitae), Labcorp | May 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at