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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-136230394-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=136230394&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MAP7D3",
"hgnc_id": 25742,
"hgvs_c": "c.1741A>T",
"hgvs_p": "p.Ile581Phe",
"inheritance_mode": "XL",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_024597.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.2436,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.11102691292762756,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 876,
"aa_ref": "I",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4385,
"cdna_start": 1783,
"cds_end": null,
"cds_length": 2631,
"cds_start": 1741,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_024597.4",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1741A>T",
"hgvs_p": "p.Ile581Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000316077.14",
"protein_coding": true,
"protein_id": "NP_078873.2",
"strand": false,
"transcript": "NM_024597.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 876,
"aa_ref": "I",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4385,
"cdna_start": 1783,
"cds_end": null,
"cds_length": 2631,
"cds_start": 1741,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000316077.14",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1741A>T",
"hgvs_p": "p.Ile581Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024597.4",
"protein_coding": true,
"protein_id": "ENSP00000318086.9",
"strand": false,
"transcript": "ENST00000316077.14",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 841,
"aa_ref": "I",
"aa_start": 546,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4365,
"cdna_start": 1649,
"cds_end": null,
"cds_length": 2526,
"cds_start": 1636,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000370661.5",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1636A>T",
"hgvs_p": "p.Ile546Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000359695.1",
"strand": false,
"transcript": "ENST00000370661.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 801,
"aa_ref": "I",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2432,
"cdna_start": 1642,
"cds_end": null,
"cds_length": 2408,
"cds_start": 1618,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000370660.3",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1618A>T",
"hgvs_p": "p.Ile540Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000359694.3",
"strand": false,
"transcript": "ENST00000370660.3",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 886,
"aa_ref": "I",
"aa_start": 591,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4379,
"cdna_start": 1784,
"cds_end": null,
"cds_length": 2661,
"cds_start": 1771,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000945657.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1771A>T",
"hgvs_p": "p.Ile591Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615716.1",
"strand": false,
"transcript": "ENST00000945657.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 876,
"aa_ref": "I",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3837,
"cdna_start": 1763,
"cds_end": null,
"cds_length": 2631,
"cds_start": 1741,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000937867.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1741A>T",
"hgvs_p": "p.Ile581Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607926.1",
"strand": false,
"transcript": "ENST00000937867.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 875,
"aa_ref": "I",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4553,
"cdna_start": 1948,
"cds_end": null,
"cds_length": 2628,
"cds_start": 1738,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000937863.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1738A>T",
"hgvs_p": "p.Ile580Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607922.1",
"strand": false,
"transcript": "ENST00000937863.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 874,
"aa_ref": "I",
"aa_start": 579,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4393,
"cdna_start": 1791,
"cds_end": null,
"cds_length": 2625,
"cds_start": 1735,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000937864.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1735A>T",
"hgvs_p": "p.Ile579Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607923.1",
"strand": false,
"transcript": "ENST00000937864.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 858,
"aa_ref": "I",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4452,
"cdna_start": 1850,
"cds_end": null,
"cds_length": 2577,
"cds_start": 1687,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001173516.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1687A>T",
"hgvs_p": "p.Ile563Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166987.1",
"strand": false,
"transcript": "NM_001173516.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 858,
"aa_ref": "I",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4446,
"cdna_start": 1850,
"cds_end": null,
"cds_length": 2577,
"cds_start": 1687,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000370663.9",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1687A>T",
"hgvs_p": "p.Ile563Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000359697.5",
"strand": false,
"transcript": "ENST00000370663.9",
"transcript_support_level": 2
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 855,
"aa_ref": "I",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3302,
"cdna_start": 1754,
"cds_end": null,
"cds_length": 2568,
"cds_start": 1741,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000937865.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1741A>T",
"hgvs_p": "p.Ile581Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607924.1",
"strand": false,
"transcript": "ENST00000937865.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 841,
"aa_ref": "I",
"aa_start": 546,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4394,
"cdna_start": 1678,
"cds_end": null,
"cds_length": 2526,
"cds_start": 1636,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001173517.2",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1636A>T",
"hgvs_p": "p.Ile546Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166988.1",
"strand": false,
"transcript": "NM_001173517.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 834,
"aa_ref": "I",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2808,
"cdna_start": 1637,
"cds_end": null,
"cds_length": 2505,
"cds_start": 1615,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000937866.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1615A>T",
"hgvs_p": "p.Ile539Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607925.1",
"strand": false,
"transcript": "ENST00000937866.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 705,
"aa_ref": "I",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2405,
"cdna_start": 1241,
"cds_end": null,
"cds_length": 2118,
"cds_start": 1228,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000945658.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1228A>T",
"hgvs_p": "p.Ile410Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615717.1",
"strand": false,
"transcript": "ENST00000945658.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 526,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000477124.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "n.517A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000477124.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2074252305",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.394,
"pos": 136230394,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.073,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_024597.4"
}
]
}