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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: 12-116019876-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=116019876&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 116019876,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000281928.9",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.722A>G",
"hgvs_p": "p.Tyr241Cys",
"transcript": "NM_015335.5",
"protein_id": "NP_056150.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 2210,
"cds_start": 722,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "ENST00000281928.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.722A>G",
"hgvs_p": "p.Tyr241Cys",
"transcript": "ENST00000281928.9",
"protein_id": "ENSP00000281928.3",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 2210,
"cds_start": 722,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "NM_015335.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.722A>G",
"hgvs_p": "p.Tyr241Cys",
"transcript": "ENST00000650226.1",
"protein_id": "ENSP00000496981.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 2222,
"cds_start": 722,
"cds_end": null,
"cds_length": 6669,
"cdna_start": 765,
"cdna_end": null,
"cdna_length": 8717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.149A>G",
"hgvs_p": "p.Tyr50Cys",
"transcript": "ENST00000549786.2",
"protein_id": "ENSP00000446782.2",
"transcript_support_level": 2,
"aa_start": 50,
"aa_end": null,
"aa_length": 1544,
"cds_start": 149,
"cds_end": null,
"cds_length": 4635,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.692A>G",
"hgvs_p": "p.Tyr231Cys",
"transcript": "ENST00000548743.2",
"protein_id": "ENSP00000448553.2",
"transcript_support_level": 3,
"aa_start": 231,
"aa_end": null,
"aa_length": 1080,
"cds_start": 692,
"cds_end": null,
"cds_length": 3244,
"cdna_start": 980,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.632A>G",
"hgvs_p": "p.Tyr211Cys",
"transcript": "ENST00000647567.1",
"protein_id": "ENSP00000497136.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 436,
"cds_start": 632,
"cds_end": null,
"cds_length": 1312,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 1312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.722A>G",
"hgvs_p": "p.Tyr241Cys",
"transcript": "XM_017019090.2",
"protein_id": "XP_016874579.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 2209,
"cds_start": 722,
"cds_end": null,
"cds_length": 6630,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 9882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.692A>G",
"hgvs_p": "p.Tyr231Cys",
"transcript": "XM_047428605.1",
"protein_id": "XP_047284561.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 2200,
"cds_start": 692,
"cds_end": null,
"cds_length": 6603,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 9514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.692A>G",
"hgvs_p": "p.Tyr231Cys",
"transcript": "XM_047428607.1",
"protein_id": "XP_047284563.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 2199,
"cds_start": 692,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 9511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.320A>G",
"hgvs_p": "p.Tyr107Cys",
"transcript": "XM_047428608.1",
"protein_id": "XP_047284564.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 2076,
"cds_start": 320,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 1046,
"cdna_end": null,
"cdna_length": 9647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.320A>G",
"hgvs_p": "p.Tyr107Cys",
"transcript": "XM_047428609.1",
"protein_id": "XP_047284565.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 2076,
"cds_start": 320,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 4416,
"cdna_end": null,
"cdna_length": 13017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.320A>G",
"hgvs_p": "p.Tyr107Cys",
"transcript": "XM_047428610.1",
"protein_id": "XP_047284566.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 2076,
"cds_start": 320,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 2213,
"cdna_end": null,
"cdna_length": 10814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.320A>G",
"hgvs_p": "p.Tyr107Cys",
"transcript": "XM_047428611.1",
"protein_id": "XP_047284567.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 2076,
"cds_start": 320,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 2309,
"cdna_end": null,
"cdna_length": 10910,
"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": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.486A>G",
"hgvs_p": null,
"transcript": "ENST00000648737.1",
"protein_id": null,
"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": 8299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"dbsnp": "rs564830776",
"frequency_reference_population": 0.0000041047983,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.0000041048,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.18186140060424805,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.163,
"revel_prediction": "Benign",
"alphamissense_score": 0.1385,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.827,
"phylop100way_prediction": "Uncertain_significance",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000281928.9",
"gene_symbol": "MED13L",
"hgnc_id": 22962,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.722A>G",
"hgvs_p": "p.Tyr241Cys"
}
],
"clinvar_disease": " dextro-looped,Transposition of the great arteries",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Transposition of the great arteries, dextro-looped",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}