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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: 4-102723865-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=102723865&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 102723865,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000647097.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg",
"transcript": "NM_005908.4",
"protein_id": "NP_005899.3",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 879,
"cds_start": 375,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "ENST00000647097.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000647097.2",
"protein_id": "ENSP00000495247.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 879,
"cds_start": 375,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "NM_005908.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000642252.1",
"protein_id": "ENSP00000495483.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 925,
"cds_start": 375,
"cds_end": null,
"cds_length": 2778,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 3342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000644159.1",
"protein_id": "ENSP00000494462.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 886,
"cds_start": 375,
"cds_end": null,
"cds_length": 2661,
"cdna_start": 463,
"cdna_end": null,
"cdna_length": 4238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000505239.1",
"protein_id": "ENSP00000427322.1",
"transcript_support_level": 2,
"aa_start": 125,
"aa_end": null,
"aa_length": 822,
"cds_start": 375,
"cds_end": null,
"cds_length": 2469,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 2577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.300A>G",
"hgvs_p": "p.Arg100Arg",
"transcript": "ENST00000646451.1",
"protein_id": "ENSP00000495846.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 198,
"cds_start": 300,
"cds_end": null,
"cds_length": 598,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 1835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.300A>G",
"hgvs_p": "p.Arg100Arg",
"transcript": "XM_047415692.1",
"protein_id": "XP_047271648.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 854,
"cds_start": 300,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 3918,
"cdna_end": null,
"cdna_length": 7470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "c.300A>G",
"hgvs_p": "p.Arg100Arg",
"transcript": "XM_047415693.1",
"protein_id": "XP_047271649.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 854,
"cds_start": 300,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 3796,
"cdna_end": null,
"cdna_length": 7348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.20A>G",
"hgvs_p": null,
"transcript": "ENST00000506478.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.422A>G",
"hgvs_p": null,
"transcript": "ENST00000514430.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.375A>G",
"hgvs_p": null,
"transcript": "ENST00000644545.1",
"protein_id": "ENSP00000493992.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.*280A>G",
"hgvs_p": null,
"transcript": "ENST00000644965.1",
"protein_id": "ENSP00000495818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.375A>G",
"hgvs_p": null,
"transcript": "ENST00000645348.1",
"protein_id": "ENSP00000495363.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.375A>G",
"hgvs_p": null,
"transcript": "ENST00000646311.1",
"protein_id": "ENSP00000493465.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.375A>G",
"hgvs_p": null,
"transcript": "ENST00000646727.1",
"protein_id": "ENSP00000493519.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.57A>G",
"hgvs_p": null,
"transcript": "ENST00000647129.1",
"protein_id": "ENSP00000496137.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.*280A>G",
"hgvs_p": null,
"transcript": "ENST00000644965.1",
"protein_id": "ENSP00000495818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"hgvs_c": "n.*341A>G",
"hgvs_p": null,
"transcript": "ENST00000511813.1",
"protein_id": "ENSP00000422001.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MANBA",
"gene_hgnc_id": 6831,
"dbsnp": "rs771587242",
"frequency_reference_population": 0.000012219074,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000121194,
"gnomad_genomes_af": 0.0000131378,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.916,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000647097.2",
"gene_symbol": "MANBA",
"hgnc_id": 6831,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.375A>G",
"hgvs_p": "p.Arg125Arg"
}
],
"clinvar_disease": "Beta-D-mannosidosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Beta-D-mannosidosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}