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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: 10-49627760-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=49627760&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 49627760,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000337653.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.1086C>T",
"hgvs_p": "p.Ala362Ala",
"transcript": "NM_020549.5",
"protein_id": "NP_065574.4",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 748,
"cds_start": 1086,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": "ENST00000337653.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.1086C>T",
"hgvs_p": "p.Ala362Ala",
"transcript": "ENST00000337653.7",
"protein_id": "ENSP00000337103.2",
"transcript_support_level": 1,
"aa_start": 362,
"aa_end": null,
"aa_length": 748,
"cds_start": 1086,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": "NM_020549.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.840C>T",
"hgvs_p": "p.Ala280Ala",
"transcript": "ENST00000395562.2",
"protein_id": "ENSP00000378929.2",
"transcript_support_level": 1,
"aa_start": 280,
"aa_end": null,
"aa_length": 666,
"cds_start": 840,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 2528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "ENST00000339797.5",
"protein_id": "ENSP00000343486.1",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 905,
"cdna_end": null,
"cdna_length": 2124,
"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": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "n.*817C>T",
"hgvs_p": null,
"transcript": "ENST00000466590.6",
"protein_id": "ENSP00000473443.1",
"transcript_support_level": 1,
"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": 2528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "n.*817C>T",
"hgvs_p": null,
"transcript": "ENST00000466590.6",
"protein_id": "ENSP00000473443.1",
"transcript_support_level": 1,
"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": 2528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.840C>T",
"hgvs_p": "p.Ala280Ala",
"transcript": "NM_001142933.2",
"protein_id": "NP_001136405.2",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 666,
"cds_start": 840,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 5366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "NM_001142929.2",
"protein_id": "NP_001136401.2",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "NM_001142934.2",
"protein_id": "NP_001136406.2",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 5366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "NM_020984.4",
"protein_id": "NP_066264.4",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 905,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "NM_020985.4",
"protein_id": "NP_066265.4",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 5134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "NM_020986.4",
"protein_id": "NP_066266.4",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 905,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "ENST00000351556.7",
"protein_id": "ENSP00000345878.3",
"transcript_support_level": 5,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 2286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Ala244Ala",
"transcript": "ENST00000395559.6",
"protein_id": "ENSP00000378926.2",
"transcript_support_level": 5,
"aa_start": 244,
"aa_end": null,
"aa_length": 630,
"cds_start": 732,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 895,
"cdna_end": null,
"cdna_length": 2114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"dbsnp": "rs374870408",
"frequency_reference_population": 0.00014747836,
"hom_count_reference_population": 0,
"allele_count_reference_population": 238,
"gnomad_exomes_af": 0.00015394,
"gnomad_genomes_af": 0.0000854195,
"gnomad_exomes_ac": 225,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.25,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.035,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000337653.7",
"gene_symbol": "CHAT",
"hgnc_id": 1912,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1086C>T",
"hgvs_p": "p.Ala362Ala"
}
],
"clinvar_disease": "Familial infantile myasthenia",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Familial infantile myasthenia",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}