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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-136227302-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=136227302&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MAP7D3",
"hgnc_id": 25742,
"hgvs_c": "c.2016C>G",
"hgvs_p": "p.Asp672Glu",
"inheritance_mode": "XL",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_024597.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.1903,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.96,
"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": 0.0747210681438446,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 876,
"aa_ref": "D",
"aa_start": 672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4385,
"cdna_start": 2058,
"cds_end": null,
"cds_length": 2631,
"cds_start": 2016,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_024597.4",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2016C>G",
"hgvs_p": "p.Asp672Glu",
"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": "E",
"aa_end": null,
"aa_length": 876,
"aa_ref": "D",
"aa_start": 672,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4385,
"cdna_start": 2058,
"cds_end": null,
"cds_length": 2631,
"cds_start": 2016,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000316077.14",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2016C>G",
"hgvs_p": "p.Asp672Glu",
"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": "E",
"aa_end": null,
"aa_length": 841,
"aa_ref": "D",
"aa_start": 637,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4365,
"cdna_start": 1924,
"cds_end": null,
"cds_length": 2526,
"cds_start": 1911,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000370661.5",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1911C>G",
"hgvs_p": "p.Asp637Glu",
"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": "E",
"aa_end": null,
"aa_length": 801,
"aa_ref": "D",
"aa_start": 631,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2432,
"cdna_start": 1917,
"cds_end": null,
"cds_length": 2408,
"cds_start": 1893,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000370660.3",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1893C>G",
"hgvs_p": "p.Asp631Glu",
"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": "E",
"aa_end": null,
"aa_length": 886,
"aa_ref": "D",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4379,
"cdna_start": 2059,
"cds_end": null,
"cds_length": 2661,
"cds_start": 2046,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000945657.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2046C>G",
"hgvs_p": "p.Asp682Glu",
"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": "E",
"aa_end": null,
"aa_length": 876,
"aa_ref": "D",
"aa_start": 672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3837,
"cdna_start": 2038,
"cds_end": null,
"cds_length": 2631,
"cds_start": 2016,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937867.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2016C>G",
"hgvs_p": "p.Asp672Glu",
"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": "E",
"aa_end": null,
"aa_length": 875,
"aa_ref": "D",
"aa_start": 671,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4553,
"cdna_start": 2223,
"cds_end": null,
"cds_length": 2628,
"cds_start": 2013,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937863.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2013C>G",
"hgvs_p": "p.Asp671Glu",
"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": "E",
"aa_end": null,
"aa_length": 874,
"aa_ref": "D",
"aa_start": 670,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4393,
"cdna_start": 2066,
"cds_end": null,
"cds_length": 2625,
"cds_start": 2010,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937864.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.2010C>G",
"hgvs_p": "p.Asp670Glu",
"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": "E",
"aa_end": null,
"aa_length": 858,
"aa_ref": "D",
"aa_start": 654,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4452,
"cdna_start": 2125,
"cds_end": null,
"cds_length": 2577,
"cds_start": 1962,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001173516.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1962C>G",
"hgvs_p": "p.Asp654Glu",
"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": "E",
"aa_end": null,
"aa_length": 858,
"aa_ref": "D",
"aa_start": 654,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4446,
"cdna_start": 2125,
"cds_end": null,
"cds_length": 2577,
"cds_start": 1962,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000370663.9",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1962C>G",
"hgvs_p": "p.Asp654Glu",
"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": "E",
"aa_end": null,
"aa_length": 855,
"aa_ref": "D",
"aa_start": 651,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3302,
"cdna_start": 1966,
"cds_end": null,
"cds_length": 2568,
"cds_start": 1953,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937865.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1953C>G",
"hgvs_p": "p.Asp651Glu",
"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": "E",
"aa_end": null,
"aa_length": 841,
"aa_ref": "D",
"aa_start": 637,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4394,
"cdna_start": 1953,
"cds_end": null,
"cds_length": 2526,
"cds_start": 1911,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001173517.2",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1911C>G",
"hgvs_p": "p.Asp637Glu",
"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": "E",
"aa_end": null,
"aa_length": 834,
"aa_ref": "D",
"aa_start": 630,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2808,
"cdna_start": 1912,
"cds_end": null,
"cds_length": 2505,
"cds_start": 1890,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937866.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1890C>G",
"hgvs_p": "p.Asp630Glu",
"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": "E",
"aa_end": null,
"aa_length": 705,
"aa_ref": "D",
"aa_start": 501,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2405,
"cdna_start": 1516,
"cds_end": null,
"cds_length": 2118,
"cds_start": 1503,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000945658.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "c.1503C>G",
"hgvs_p": "p.Asp501Glu",
"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": 502,
"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": "ENST00000489788.5",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "n.132C>G",
"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": "ENST00000489788.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 774,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000495432.1",
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"hgvs_c": "n.503C>G",
"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": "ENST00000495432.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1046459058",
"effect": "missense_variant",
"frequency_reference_population": 0.0000058060014,
"gene_hgnc_id": 25742,
"gene_symbol": "MAP7D3",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000455587,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000184904,
"gnomad_genomes_homalt": 0,
"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": -0.429,
"pos": 136227302,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.074,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024597.4"
}
]
}