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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: 4-118815546-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=118815546&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 118815546,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001318066.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "NM_014822.4",
"protein_id": "NP_055637.2",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1032,
"cds_start": 578,
"cds_end": null,
"cds_length": 3099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000280551.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014822.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000280551.11",
"protein_id": "ENSP00000280551.6",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 1032,
"cds_start": 578,
"cds_end": null,
"cds_length": 3099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014822.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000280551.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "ENST00000509818.5",
"protein_id": "ENSP00000424085.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000509818.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.*552C>T",
"hgvs_p": null,
"transcript": "ENST00000514561.5",
"protein_id": "ENSP00000422717.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000514561.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.*552C>T",
"hgvs_p": null,
"transcript": "ENST00000514561.5",
"protein_id": "ENSP00000422717.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000514561.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "NM_001318066.2",
"protein_id": "NP_001304995.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1033,
"cds_start": 578,
"cds_end": null,
"cds_length": 3102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318066.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000924655.1",
"protein_id": "ENSP00000594714.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1032,
"cds_start": 578,
"cds_end": null,
"cds_length": 3099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924655.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000924658.1",
"protein_id": "ENSP00000594717.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1032,
"cds_start": 578,
"cds_end": null,
"cds_length": 3099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924658.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000924656.1",
"protein_id": "ENSP00000594715.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1031,
"cds_start": 578,
"cds_end": null,
"cds_length": 3096,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924656.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000899696.1",
"protein_id": "ENSP00000569755.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 994,
"cds_start": 578,
"cds_end": null,
"cds_length": 2985,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899696.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000899695.1",
"protein_id": "ENSP00000569754.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 993,
"cds_start": 578,
"cds_end": null,
"cds_length": 2982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899695.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000924657.1",
"protein_id": "ENSP00000594716.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 936,
"cds_start": 578,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924657.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.-755C>T",
"hgvs_p": null,
"transcript": "ENST00000419654.6",
"protein_id": "ENSP00000388324.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": null,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419654.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.685C>T",
"hgvs_p": null,
"transcript": "ENST00000506622.5",
"protein_id": "ENSP00000427249.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000506622.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.*81C>T",
"hgvs_p": null,
"transcript": "ENST00000503683.1",
"protein_id": "ENSP00000426309.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": null,
"cds_end": null,
"cds_length": 497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503683.1"
}
],
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"dbsnp": "rs6844109",
"frequency_reference_population": 0.001748295,
"hom_count_reference_population": 17,
"allele_count_reference_population": 2822,
"gnomad_exomes_af": 0.00137222,
"gnomad_genomes_af": 0.00535862,
"gnomad_exomes_ac": 2006,
"gnomad_genomes_ac": 816,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004474937915802002,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.221,
"revel_prediction": "Benign",
"alphamissense_score": 0.0994,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.519,
"phylop100way_prediction": "Benign",
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001318066.2",
"gene_symbol": "SEC24D",
"hgnc_id": 10706,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}