NM_004371.4:c.3615+49A>G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004371.4(COPA):c.3615+49A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,567,586 control chromosomes in the GnomAD database, including 194,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004371.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COPA | NM_004371.4 | c.3615+49A>G | intron_variant | Intron 32 of 32 | ENST00000241704.8 | NP_004362.2 | ||
COPA | NM_001098398.2 | c.3642+49A>G | intron_variant | Intron 32 of 32 | NP_001091868.1 | |||
LOC107985219 | XR_001738265.2 | n.537-814T>C | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.428 AC: 65043AN: 151796Hom.: 14905 Cov.: 31
GnomAD3 exomes AF: 0.480 AC: 109495AN: 227936Hom.: 27240 AF XY: 0.492 AC XY: 60683AN XY: 123370
GnomAD4 exome AF: 0.500 AC: 707195AN: 1415670Hom.: 179412 Cov.: 27 AF XY: 0.503 AC XY: 352835AN XY: 701400
GnomAD4 genome AF: 0.428 AC: 65067AN: 151916Hom.: 14904 Cov.: 31 AF XY: 0.430 AC XY: 31937AN XY: 74236
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 74% of patients studied by a panel of primary immunodeficiencies. Number of patients: 71. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at