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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: 19-42375804-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=42375804&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 42375804,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000251268.11",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.7567A>G",
"hgvs_p": "p.Thr2523Ala",
"transcript": "NM_001271938.2",
"protein_id": "NP_001258867.1",
"transcript_support_level": null,
"aa_start": 2523,
"aa_end": null,
"aa_length": 2845,
"cds_start": 7567,
"cds_end": null,
"cds_length": 8538,
"cdna_start": 8176,
"cdna_end": null,
"cdna_length": 11137,
"mane_select": "ENST00000251268.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.7567A>G",
"hgvs_p": "p.Thr2523Ala",
"transcript": "ENST00000251268.11",
"protein_id": "ENSP00000251268.5",
"transcript_support_level": 5,
"aa_start": 2523,
"aa_end": null,
"aa_length": 2845,
"cds_start": 7567,
"cds_end": null,
"cds_length": 8538,
"cdna_start": 8176,
"cdna_end": null,
"cdna_length": 11137,
"mane_select": "NM_001271938.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.7366A>G",
"hgvs_p": "p.Thr2456Ala",
"transcript": "ENST00000334370.8",
"protein_id": "ENSP00000334219.4",
"transcript_support_level": 1,
"aa_start": 2456,
"aa_end": null,
"aa_length": 2778,
"cds_start": 7366,
"cds_end": null,
"cds_length": 8337,
"cdna_start": 8001,
"cdna_end": null,
"cdna_length": 10966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.*156A>G",
"hgvs_p": null,
"transcript": "ENST00000593647.1",
"protein_id": "ENSP00000470620.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": -4,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.7366A>G",
"hgvs_p": "p.Thr2456Ala",
"transcript": "NM_001410.3",
"protein_id": "NP_001401.2",
"transcript_support_level": null,
"aa_start": 2456,
"aa_end": null,
"aa_length": 2778,
"cds_start": 7366,
"cds_end": null,
"cds_length": 8337,
"cdna_start": 7975,
"cdna_end": null,
"cdna_length": 10936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.349A>G",
"hgvs_p": "p.Thr117Ala",
"transcript": "ENST00000378073.5",
"protein_id": "ENSP00000367313.4",
"transcript_support_level": 5,
"aa_start": 117,
"aa_end": null,
"aa_length": 439,
"cds_start": 349,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 8069,
"cdna_end": null,
"cdna_length": 11034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "n.502A>G",
"hgvs_p": null,
"transcript": "ENST00000599787.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"hgvs_c": "c.160-2896A>G",
"hgvs_p": null,
"transcript": "ENST00000598762.1",
"protein_id": "ENSP00000471370.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 69,
"cds_start": -4,
"cds_end": null,
"cds_length": 210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MEGF8",
"gene_hgnc_id": 3233,
"dbsnp": "rs139192223",
"frequency_reference_population": 0.00094695325,
"hom_count_reference_population": 2,
"allele_count_reference_population": 1527,
"gnomad_exomes_af": 0.000967457,
"gnomad_genomes_af": 0.000749951,
"gnomad_exomes_ac": 1413,
"gnomad_genomes_ac": 114,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00582432746887207,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.0594,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.529,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000251268.11",
"gene_symbol": "MEGF8",
"hgnc_id": 3233,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7567A>G",
"hgvs_p": "p.Thr2523Ala"
}
],
"clinvar_disease": "MEGF8-related Carpenter syndrome,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "MEGF8-related Carpenter syndrome|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}