1-160290574-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3BP6BS1BS2
The NM_004371.4(COPA):c.3533G>A(p.Arg1178His) variant causes a missense change. The variant allele was found at a frequency of 0.0000328 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1178C) has been classified as Uncertain significance.
Frequency
Consequence
NM_004371.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COPA | NM_004371.4 | c.3533G>A | p.Arg1178His | missense_variant | Exon 32 of 33 | ENST00000241704.8 | NP_004362.2 | |
COPA | NM_001098398.2 | c.3560G>A | p.Arg1187His | missense_variant | Exon 32 of 33 | NP_001091868.1 | ||
LOC107985219 | XR_001738265.2 | n.537-683C>T | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251446Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135890
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 727248
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
Autoimmune interstitial lung disease-arthritis syndrome Benign:1Other:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 06, 2024 | - - |
not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | Variant interpreted as Uncertain significance and reported on 03-04-2021 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.3560G>A (p.R1187H) alteration is located in exon 32 (coding exon 32) of the COPA gene. This alteration results from a G to A substitution at nucleotide position 3560, causing the arginine (R) at amino acid position 1187 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at