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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: 10-49622125-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=49622125&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 49622125,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000337653.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.727C>T",
"hgvs_p": "p.Leu243Phe",
"transcript": "NM_020549.5",
"protein_id": "NP_065574.4",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 748,
"cds_start": 727,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": "ENST00000337653.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.727C>T",
"hgvs_p": "p.Leu243Phe",
"transcript": "ENST00000337653.7",
"protein_id": "ENSP00000337103.2",
"transcript_support_level": 1,
"aa_start": 243,
"aa_end": null,
"aa_length": 748,
"cds_start": 727,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": "NM_020549.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Leu161Phe",
"transcript": "ENST00000395562.2",
"protein_id": "ENSP00000378929.2",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 666,
"cds_start": 481,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 2528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "ENST00000339797.5",
"protein_id": "ENSP00000343486.1",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 546,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "n.708C>T",
"hgvs_p": null,
"transcript": "ENST00000460699.5",
"protein_id": null,
"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": 749,
"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": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "n.*458C>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": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "n.*458C>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": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Leu161Phe",
"transcript": "NM_001142933.2",
"protein_id": "NP_001136405.2",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 666,
"cds_start": 481,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 5366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "NM_001142929.2",
"protein_id": "NP_001136401.2",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "NM_001142934.2",
"protein_id": "NP_001136406.2",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 5366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "NM_020984.4",
"protein_id": "NP_066264.4",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 546,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "NM_020985.4",
"protein_id": "NP_066265.4",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 5134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "NM_020986.4",
"protein_id": "NP_066266.4",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 546,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "ENST00000351556.7",
"protein_id": "ENSP00000345878.3",
"transcript_support_level": 5,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 708,
"cdna_end": null,
"cdna_length": 2286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Leu125Phe",
"transcript": "ENST00000395559.6",
"protein_id": "ENSP00000378926.2",
"transcript_support_level": 5,
"aa_start": 125,
"aa_end": null,
"aa_length": 630,
"cds_start": 373,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 536,
"cdna_end": null,
"cdna_length": 2114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHAT",
"gene_hgnc_id": 1912,
"dbsnp": "rs8178990",
"frequency_reference_population": 0.056620073,
"hom_count_reference_population": 3079,
"allele_count_reference_population": 91165,
"gnomad_exomes_af": 0.0577444,
"gnomad_genomes_af": 0.0457872,
"gnomad_exomes_ac": 84233,
"gnomad_genomes_ac": 6932,
"gnomad_exomes_homalt": 2826,
"gnomad_genomes_homalt": 253,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003634721040725708,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.733,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3815,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.052,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000337653.7",
"gene_symbol": "CHAT",
"hgnc_id": 1912,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.727C>T",
"hgvs_p": "p.Leu243Phe"
}
],
"clinvar_disease": "Familial infantile myasthenia,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:5",
"phenotype_combined": "not specified|Familial infantile myasthenia|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}