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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-77830846-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77830846&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MAGT1",
"hgnc_id": 28880,
"hgvs_c": "c.1047G>A",
"hgvs_p": "p.Met349Ile",
"inheritance_mode": "XL,Unknown",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_032121.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.5156,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "X",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.35089415311813354,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 335,
"aa_ref": "M",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4506,
"cdna_start": 976,
"cds_end": null,
"cds_length": 1008,
"cds_start": 951,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001367916.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.951G>A",
"hgvs_p": "p.Met317Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000618282.5",
"protein_coding": true,
"protein_id": "NP_001354845.1",
"strand": false,
"transcript": "NM_001367916.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 335,
"aa_ref": "M",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4506,
"cdna_start": 976,
"cds_end": null,
"cds_length": 1008,
"cds_start": 951,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000618282.5",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.951G>A",
"hgvs_p": "p.Met317Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001367916.1",
"protein_coding": true,
"protein_id": "ENSP00000480732.1",
"strand": false,
"transcript": "ENST00000618282.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 335,
"aa_ref": "M",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4047,
"cdna_start": 1134,
"cds_end": null,
"cds_length": 1008,
"cds_start": 951,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000358075.11",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.951G>A",
"hgvs_p": "p.Met317Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000354649.6",
"strand": false,
"transcript": "ENST00000358075.11",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 367,
"aa_ref": "M",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4022,
"cdna_start": 1109,
"cds_end": null,
"cds_length": 1104,
"cds_start": 1047,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_032121.5",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.1047G>A",
"hgvs_p": "p.Met349Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_115497.4",
"strand": false,
"transcript": "NM_032121.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 305,
"aa_ref": "M",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3472,
"cdna_start": 888,
"cds_end": null,
"cds_length": 918,
"cds_start": 861,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000688650.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.861G>A",
"hgvs_p": "p.Met287Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509785.1",
"strand": false,
"transcript": "ENST00000688650.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 288,
"aa_ref": "M",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3853,
"cdna_start": 944,
"cds_end": null,
"cds_length": 867,
"cds_start": 810,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000944450.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.810G>A",
"hgvs_p": "p.Met270Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000614509.1",
"strand": false,
"transcript": "ENST00000944450.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 241,
"aa_ref": "M",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3596,
"cdna_start": 707,
"cds_end": null,
"cds_length": 726,
"cds_start": 669,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000692161.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Met223Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509676.1",
"strand": false,
"transcript": "ENST00000692161.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 312,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1329,
"cdna_start": null,
"cds_end": null,
"cds_length": 939,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000685015.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.902-4037G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509969.1",
"strand": false,
"transcript": "ENST00000685015.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 302,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2729,
"cdna_start": null,
"cds_end": null,
"cds_length": 909,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000689519.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.902-1611G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509887.1",
"strand": false,
"transcript": "ENST00000689519.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 272,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2480,
"cdna_start": null,
"cds_end": null,
"cds_length": 819,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000685353.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "c.812-1611G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510266.1",
"strand": false,
"transcript": "ENST00000685353.1",
"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": 2103,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000689137.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "n.849G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509458.1",
"strand": false,
"transcript": "ENST00000689137.1",
"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": 2535,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000691172.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "n.849G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508529.1",
"strand": false,
"transcript": "ENST00000691172.1",
"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": 3407,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000691993.1",
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"hgvs_c": "n.1047G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509067.1",
"strand": false,
"transcript": "ENST00000691993.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2076895504",
"effect": "missense_variant",
"frequency_reference_population": 9.541748e-7,
"gene_hgnc_id": 28880,
"gene_symbol": "MAGT1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 9.54175e-7,
"gnomad_exomes_homalt": 0,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.114,
"pos": 77830846,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.206,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_032121.5"
}
]
}