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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: 3-148996406-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=148996406&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 148996406,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000345003.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "NM_004130.4",
"protein_id": "NP_004121.2",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 350,
"cds_start": 248,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 5996,
"mane_select": "ENST00000345003.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000345003.9",
"protein_id": "ENSP00000340736.4",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 350,
"cds_start": 248,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 5996,
"mane_select": "NM_004130.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000296048.10",
"protein_id": "ENSP00000296048.6",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 333,
"cds_start": 248,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 1890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000484197.5",
"protein_id": "ENSP00000420683.1",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 279,
"cds_start": 248,
"cds_end": null,
"cds_length": 840,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 1563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "NM_001184720.2",
"protein_id": "NP_001171649.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 333,
"cds_start": 248,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 5945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "NM_001184721.2",
"protein_id": "NP_001171650.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 279,
"cds_start": 248,
"cds_end": null,
"cds_length": 840,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 5725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000461191.1",
"protein_id": "ENSP00000420247.1",
"transcript_support_level": 2,
"aa_start": 83,
"aa_end": null,
"aa_length": 264,
"cds_start": 248,
"cds_end": null,
"cds_length": 797,
"cdna_start": 317,
"cdna_end": null,
"cdna_length": 866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000483267.5",
"protein_id": "ENSP00000419499.1",
"transcript_support_level": 2,
"aa_start": 83,
"aa_end": null,
"aa_length": 193,
"cds_start": 248,
"cds_end": null,
"cds_length": 582,
"cdna_start": 377,
"cdna_end": null,
"cdna_length": 801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys",
"transcript": "ENST00000627418.2",
"protein_id": "ENSP00000486061.1",
"transcript_support_level": 5,
"aa_start": 83,
"aa_end": null,
"aa_length": 193,
"cds_start": 248,
"cds_end": null,
"cds_length": 582,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 1831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.110C>A",
"hgvs_p": "p.Thr37Lys",
"transcript": "ENST00000492285.6",
"protein_id": "ENSP00000418297.2",
"transcript_support_level": 4,
"aa_start": 37,
"aa_end": null,
"aa_length": 109,
"cds_start": 110,
"cds_end": null,
"cds_length": 331,
"cdna_start": 436,
"cdna_end": null,
"cdna_length": 657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.110C>A",
"hgvs_p": "p.Thr37Lys",
"transcript": "ENST00000473005.1",
"protein_id": "ENSP00000417671.1",
"transcript_support_level": 3,
"aa_start": 37,
"aa_end": null,
"aa_length": 59,
"cds_start": 110,
"cds_end": null,
"cds_length": 180,
"cdna_start": 643,
"cdna_end": null,
"cdna_length": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.71C>A",
"hgvs_p": "p.Thr24Lys",
"transcript": "XM_017006275.2",
"protein_id": "XP_016861764.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 274,
"cds_start": 71,
"cds_end": null,
"cds_length": 825,
"cdna_start": 213,
"cdna_end": null,
"cdna_length": 5809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "n.141C>A",
"hgvs_p": null,
"transcript": "ENST00000465547.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "n.349C>A",
"hgvs_p": null,
"transcript": "ENST00000478067.1",
"protein_id": null,
"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": 476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"dbsnp": "rs267606858",
"frequency_reference_population": 0.000006571252,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657125,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.907111406326294,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.572,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9779,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.542,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000345003.9",
"gene_symbol": "GYG1",
"hgnc_id": 4699,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Thr83Lys"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}