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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: 4-118723649-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=118723649&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 118723649,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001318066.2",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2965A>G",
"hgvs_p": "p.Ile989Val",
"transcript": "NM_014822.4",
"protein_id": "NP_055637.2",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2965,
"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": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2965A>G",
"hgvs_p": "p.Ile989Val",
"transcript": "ENST00000280551.11",
"protein_id": "ENSP00000280551.6",
"transcript_support_level": 1,
"aa_start": 989,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2965,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.1858A>G",
"hgvs_p": "p.Ile620Val",
"transcript": "ENST00000511481.5",
"protein_id": "ENSP00000425491.1",
"transcript_support_level": 1,
"aa_start": 620,
"aa_end": null,
"aa_length": 663,
"cds_start": 1858,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511481.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2968A>G",
"hgvs_p": "p.Ile990Val",
"transcript": "NM_001318066.2",
"protein_id": "NP_001304995.1",
"transcript_support_level": null,
"aa_start": 990,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2968,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2965A>G",
"hgvs_p": "p.Ile989Val",
"transcript": "ENST00000924655.1",
"protein_id": "ENSP00000594714.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2965,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2965A>G",
"hgvs_p": "p.Ile989Val",
"transcript": "ENST00000924658.1",
"protein_id": "ENSP00000594717.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2965,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2962A>G",
"hgvs_p": "p.Ile988Val",
"transcript": "ENST00000924656.1",
"protein_id": "ENSP00000594715.1",
"transcript_support_level": null,
"aa_start": 988,
"aa_end": null,
"aa_length": 1031,
"cds_start": 2962,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2851A>G",
"hgvs_p": "p.Ile951Val",
"transcript": "ENST00000899696.1",
"protein_id": "ENSP00000569755.1",
"transcript_support_level": null,
"aa_start": 951,
"aa_end": null,
"aa_length": 994,
"cds_start": 2851,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2848A>G",
"hgvs_p": "p.Ile950Val",
"transcript": "ENST00000899695.1",
"protein_id": "ENSP00000569754.1",
"transcript_support_level": null,
"aa_start": 950,
"aa_end": null,
"aa_length": 993,
"cds_start": 2848,
"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": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Ile893Val",
"transcript": "ENST00000924657.1",
"protein_id": "ENSP00000594716.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 936,
"cds_start": 2677,
"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": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.294A>G",
"hgvs_p": null,
"transcript": "ENST00000502830.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000502830.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"hgvs_c": "n.3096A>G",
"hgvs_p": null,
"transcript": "ENST00000505134.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000505134.5"
}
],
"gene_symbol": "SEC24D",
"gene_hgnc_id": 10706,
"dbsnp": "rs1725258764",
"frequency_reference_population": 0.000006584926,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000658493,
"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": 0.07698819041252136,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.014,
"revel_prediction": "Benign",
"alphamissense_score": 0.0529,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.727,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001318066.2",
"gene_symbol": "SEC24D",
"hgnc_id": 10706,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2968A>G",
"hgvs_p": "p.Ile990Val"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}