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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: 20-45293992-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=45293992&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MATN4",
"hgnc_id": 6910,
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_003833.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 20,
"alphamissense_prediction": null,
"alphamissense_score": 0.1285,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.24,
"chr": "20",
"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": 0.21261835098266602,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2222,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001393530.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372756.6",
"protein_coding": true,
"protein_id": "NP_001380459.1",
"strand": false,
"transcript": "NM_001393530.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2222,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000372756.6",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001393530.1",
"protein_coding": true,
"protein_id": "ENSP00000361842.1",
"strand": false,
"transcript": "ENST00000372756.6",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 622,
"aa_ref": "E",
"aa_start": 576,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2200,
"cdna_start": 1735,
"cds_end": null,
"cds_length": 1869,
"cds_start": 1726,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000372754.5",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1726G>A",
"hgvs_p": "p.Glu576Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000361840.1",
"strand": false,
"transcript": "ENST00000372754.5",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 540,
"aa_ref": "E",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2127,
"cdna_start": 1667,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000360607.10",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Glu494Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000353819.5",
"strand": false,
"transcript": "ENST00000360607.10",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2308,
"cdna_start": 1848,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_003833.5",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_003824.2",
"strand": false,
"transcript": "NM_003833.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2313,
"cdna_start": 1848,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000537548.3",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000440328.1",
"strand": false,
"transcript": "ENST00000537548.3",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3047,
"cdna_start": 2585,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000922695.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592754.1",
"strand": false,
"transcript": "ENST00000922695.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 581,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3032,
"cdna_start": 2572,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000922696.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592755.1",
"strand": false,
"transcript": "ENST00000922696.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 575,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2304,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 1728,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001393531.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001380460.1",
"strand": false,
"transcript": "NM_001393531.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 540,
"aa_ref": "E",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2099,
"cdna_start": 1639,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_030590.4",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Glu494Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_085080.1",
"strand": false,
"transcript": "NM_030590.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 540,
"aa_ref": "E",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2208,
"cdna_start": 1743,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000874026.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Glu494Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544085.1",
"strand": false,
"transcript": "ENST00000874026.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 540,
"aa_ref": "E",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2800,
"cdna_start": 2341,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000922697.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Glu494Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592756.1",
"strand": false,
"transcript": "ENST00000922697.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 499,
"aa_ref": "E",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1976,
"cdna_start": 1516,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_030592.4",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1357G>A",
"hgvs_p": "p.Glu453Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_085095.1",
"strand": false,
"transcript": "NM_030592.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 499,
"aa_ref": "E",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1979,
"cdna_start": 1514,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000353917.10",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1357G>A",
"hgvs_p": "p.Glu453Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000243983.5",
"strand": false,
"transcript": "ENST00000353917.10",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 575,
"aa_ref": "E",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2545,
"cdna_start": 2003,
"cds_end": null,
"cds_length": 1728,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017028113.2",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1603G>A",
"hgvs_p": "p.Glu535Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883602.1",
"strand": false,
"transcript": "XM_017028113.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 534,
"aa_ref": "E",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2181,
"cdna_start": 1639,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017028114.2",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Glu494Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883603.1",
"strand": false,
"transcript": "XM_017028114.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 493,
"aa_ref": "E",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": 1516,
"cds_end": null,
"cds_length": 1482,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017028115.2",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1357G>A",
"hgvs_p": "p.Glu453Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883604.1",
"strand": false,
"transcript": "XM_017028115.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 493,
"aa_ref": "E",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2299,
"cdna_start": 1757,
"cds_end": null,
"cds_length": 1482,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047440576.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "c.1357G>A",
"hgvs_p": "p.Glu453Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296532.1",
"strand": false,
"transcript": "XM_047440576.1",
"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": 1817,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000686119.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "n.*1410G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510496.1",
"strand": false,
"transcript": "ENST00000686119.1",
"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": 1817,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000686119.1",
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"hgvs_c": "n.*1410G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510496.1",
"strand": false,
"transcript": "ENST00000686119.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs769837832",
"effect": "missense_variant",
"frequency_reference_population": 0.000012479082,
"gene_hgnc_id": 6910,
"gene_symbol": "MATN4",
"gnomad_exomes_ac": 16,
"gnomad_exomes_af": 0.0000110313,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262712,
"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": "Uncertain_significance",
"phylop100way_score": 4.229,
"pos": 45293992,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.538,
"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_003833.5"
}
]
}