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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: X-154379690-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=154379690&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "EMD",
"hgnc_id": 3331,
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"inheritance_mode": "XL",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_000117.3",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_score": 8,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7775,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.22,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "X-linked Emery-Dreifuss muscular dystrophy",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9646188020706177,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1281,
"cdna_start": 273,
"cds_end": null,
"cds_length": 765,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_000117.3",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000369842.9",
"protein_coding": true,
"protein_id": "NP_000108.1",
"strand": true,
"transcript": "NM_000117.3",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1281,
"cdna_start": 273,
"cds_end": null,
"cds_length": 765,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000369842.9",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000117.3",
"protein_coding": true,
"protein_id": "ENSP00000358857.4",
"strand": true,
"transcript": "ENST00000369842.9",
"transcript_support_level": 1
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 263,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1359,
"cdna_start": 324,
"cds_end": null,
"cds_length": 792,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000933532.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603591.1",
"strand": true,
"transcript": "ENST00000933532.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 262,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1195,
"cdna_start": 163,
"cds_end": null,
"cds_length": 789,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000933533.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603592.1",
"strand": true,
"transcript": "ENST00000933533.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 987,
"cdna_start": 83,
"cds_end": null,
"cds_length": 765,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000683627.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000507533.1",
"strand": true,
"transcript": "ENST00000683627.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 215,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 776,
"cdna_start": 151,
"cds_end": null,
"cds_length": 648,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000682114.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000507245.1",
"strand": true,
"transcript": "ENST00000682114.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 165,
"aa_ref": "G",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 979,
"cdna_start": 240,
"cds_end": null,
"cds_length": 498,
"cds_start": 83,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000897866.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.83G>A",
"hgvs_p": "p.Gly28Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567925.1",
"strand": true,
"transcript": "ENST00000897866.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 219,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 966,
"cdna_start": null,
"cds_end": null,
"cds_length": 660,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000369835.3",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "c.82+124G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358850.3",
"strand": true,
"transcript": "ENST00000369835.3",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 946,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000428228.5",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.54G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000401081.1",
"strand": true,
"transcript": "ENST00000428228.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000468294.5",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.43G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000468294.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1284,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000486738.5",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.227G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000486738.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 832,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000492448.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.66G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492448.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 765,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000494443.5",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.140G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000494443.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000682478.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.59G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000682478.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1281,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000683576.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.59G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000683576.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 798,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000684082.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.83G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508266.1",
"strand": true,
"transcript": "ENST00000684082.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1114,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000684633.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.55G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000684633.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 704,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000684678.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.79G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000507059.1",
"strand": true,
"transcript": "ENST00000684678.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 792,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000485261.1",
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"hgvs_c": "n.163+124G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000485261.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.920074255878954,
"dbsnp": "rs781978021",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 3331,
"gene_symbol": "EMD",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "X-linked Emery-Dreifuss muscular dystrophy",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.673,
"pos": 154379690,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.407,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.6480000019073486,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.1,
"transcript": "NM_000117.3"
}
]
}