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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: 2-130182444-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=130182444&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MZT2B",
"hgnc_id": 25886,
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_001330282.2",
"verdict": "Benign"
},
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "SMPD4",
"hgnc_id": 32949,
"hgvs_c": "c.-843G>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "ENST00000409031.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1,BS2",
"acmg_score": -14,
"allele_count_reference_population": 4051,
"alphamissense_prediction": null,
"alphamissense_score": 0.2918,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "2",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.00685042142868042,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 158,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 599,
"cdna_start": 183,
"cds_end": null,
"cds_length": 477,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_025029.5",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000281871.11",
"protein_coding": true,
"protein_id": "NP_079305.2",
"strand": true,
"transcript": "NM_025029.5",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 158,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 599,
"cdna_start": 183,
"cds_end": null,
"cds_length": 477,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000281871.11",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025029.5",
"protein_coding": true,
"protein_id": "ENSP00000281871.7",
"strand": true,
"transcript": "ENST00000281871.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 866,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4896,
"cdna_start": null,
"cds_end": null,
"cds_length": 2601,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000409031.5",
"gene_hgnc_id": 32949,
"gene_symbol": "SMPD4",
"hgvs_c": "c.-843G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386531.1",
"strand": false,
"transcript": "ENST00000409031.5",
"transcript_support_level": 1
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 218,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 779,
"cdna_start": 183,
"cds_end": null,
"cds_length": 657,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001330282.2",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317211.1",
"strand": true,
"transcript": "NM_001330282.2",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 218,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 769,
"cdna_start": 188,
"cds_end": null,
"cds_length": 657,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000409255.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386419.1",
"strand": true,
"transcript": "ENST00000409255.1",
"transcript_support_level": 5
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 175,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 631,
"cdna_start": 178,
"cds_end": null,
"cds_length": 528,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000916359.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586418.1",
"strand": true,
"transcript": "ENST00000916359.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 130,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": 183,
"cds_end": null,
"cds_length": 393,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001330284.2",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317213.1",
"strand": true,
"transcript": "NM_001330284.2",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 120,
"aa_ref": "D",
"aa_start": 44,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 401,
"cdna_start": 132,
"cds_end": null,
"cds_length": 363,
"cds_start": 132,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000455239.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.132C>A",
"hgvs_p": "p.Asp44Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000404629.1",
"strand": true,
"transcript": "ENST00000455239.1",
"transcript_support_level": 2
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 153,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1080,
"cdna_start": 183,
"cds_end": null,
"cds_length": 462,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047445914.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301870.1",
"strand": true,
"transcript": "XM_047445914.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 132,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1558,
"cdna_start": 183,
"cds_end": null,
"cds_length": 399,
"cds_start": 162,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047445916.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301872.1",
"strand": true,
"transcript": "XM_047445916.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 156,
"aa_ref": "D",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 603,
"cdna_start": 221,
"cds_end": null,
"cds_length": 471,
"cds_start": 162,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000651060.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.162C>A",
"hgvs_p": "p.Asp54Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498754.1",
"strand": true,
"transcript": "ENST00000651060.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 827,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5314,
"cdna_start": null,
"cds_end": null,
"cds_length": 2484,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000883567.1",
"gene_hgnc_id": 32949,
"gene_symbol": "SMPD4",
"hgvs_c": "c.-226G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553626.1",
"strand": false,
"transcript": "ENST00000883567.1",
"transcript_support_level": null
},
{
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"aa_length": 201,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 702,
"cdna_start": null,
"cds_end": null,
"cds_length": 606,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000948926.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.119+43C>A",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618985.1",
"strand": true,
"transcript": "ENST00000948926.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 545,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
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"feature": "ENST00000916358.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.119+43C>A",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000586417.1",
"strand": true,
"transcript": "ENST00000916358.1",
"transcript_support_level": null
},
{
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"aa_length": 121,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 455,
"cdna_start": null,
"cds_end": null,
"cds_length": 366,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000425361.5",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.60-183C>A",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398749.1",
"strand": true,
"transcript": "ENST00000425361.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 121,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 435,
"cdna_start": null,
"cds_end": null,
"cds_length": 366,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000457492.5",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.60-183C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000387805.1",
"strand": true,
"transcript": "ENST00000457492.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 552,
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"cds_end": null,
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"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
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"feature": "XM_047445915.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "c.37-183C>A",
"hgvs_p": null,
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"protein_coding": true,
"protein_id": "XP_047301871.1",
"strand": true,
"transcript": "XM_047445915.1",
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},
{
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"biotype": "retained_intron",
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"cdna_end": null,
"cdna_length": 583,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000485869.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "n.30C>A",
"hgvs_p": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000485869.1",
"transcript_support_level": 2
},
{
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"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 480,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000480182.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "n.-111C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000480182.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 234,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000491178.1",
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"hgvs_c": "n.-236C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000491178.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201954757",
"effect": "missense_variant",
"frequency_reference_population": 0.0025976307,
"gene_hgnc_id": 25886,
"gene_symbol": "MZT2B",
"gnomad_exomes_ac": 3205,
"gnomad_exomes_af": 0.00227749,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_ac": 846,
"gnomad_genomes_af": 0.0055568,
"gnomad_genomes_homalt": 7,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 27,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.109,
"pos": 130182444,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.069,
"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_001330282.2"
}
]
}