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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: 5-163469774-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=163469774&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 163469774,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001142556.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.407C>T",
"hgvs_p": "p.Thr136Ile",
"transcript": "NM_001142556.2",
"protein_id": "NP_001136028.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 725,
"cds_start": 407,
"cds_end": null,
"cds_length": 2178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393915.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142556.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.407C>T",
"hgvs_p": "p.Thr136Ile",
"transcript": "ENST00000393915.9",
"protein_id": "ENSP00000377492.4",
"transcript_support_level": 1,
"aa_start": 136,
"aa_end": null,
"aa_length": 725,
"cds_start": 407,
"cds_end": null,
"cds_length": 2178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001142556.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393915.9"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.404C>T",
"hgvs_p": "p.Thr135Ile",
"transcript": "ENST00000358715.3",
"protein_id": "ENSP00000351554.3",
"transcript_support_level": 1,
"aa_start": 135,
"aa_end": null,
"aa_length": 724,
"cds_start": 404,
"cds_end": null,
"cds_length": 2175,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358715.3"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.359C>T",
"hgvs_p": "p.Thr120Ile",
"transcript": "ENST00000353866.7",
"protein_id": "ENSP00000185942.6",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 709,
"cds_start": 359,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353866.7"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.62C>T",
"hgvs_p": "p.Thr21Ile",
"transcript": "ENST00000520345.5",
"protein_id": "ENSP00000428481.1",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 100,
"cds_start": 62,
"cds_end": null,
"cds_length": 305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000520345.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.404C>T",
"hgvs_p": "p.Thr135Ile",
"transcript": "NM_012484.3",
"protein_id": "NP_036616.2",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 724,
"cds_start": 404,
"cds_end": null,
"cds_length": 2175,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012484.3"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.359C>T",
"hgvs_p": "p.Thr120Ile",
"transcript": "NM_012485.3",
"protein_id": "NP_036617.2",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 709,
"cds_start": 359,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012485.3"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.359C>T",
"hgvs_p": "p.Thr120Ile",
"transcript": "ENST00000932207.1",
"protein_id": "ENSP00000602266.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 708,
"cds_start": 359,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932207.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.341C>T",
"hgvs_p": "p.Thr114Ile",
"transcript": "ENST00000932208.1",
"protein_id": "ENSP00000602267.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 703,
"cds_start": 341,
"cds_end": null,
"cds_length": 2112,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932208.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.146C>T",
"hgvs_p": "p.Thr49Ile",
"transcript": "NM_001142557.2",
"protein_id": "NP_001136029.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 638,
"cds_start": 146,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142557.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.146C>T",
"hgvs_p": "p.Thr49Ile",
"transcript": "ENST00000432118.6",
"protein_id": "ENSP00000402673.2",
"transcript_support_level": 2,
"aa_start": 49,
"aa_end": null,
"aa_length": 638,
"cds_start": 146,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000432118.6"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.407C>T",
"hgvs_p": "p.Thr136Ile",
"transcript": "ENST00000932209.1",
"protein_id": "ENSP00000602268.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 637,
"cds_start": 407,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932209.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "c.62C>T",
"hgvs_p": "p.Thr21Ile",
"transcript": "ENST00000522094.5",
"protein_id": "ENSP00000428406.1",
"transcript_support_level": 4,
"aa_start": 21,
"aa_end": null,
"aa_length": 91,
"cds_start": 62,
"cds_end": null,
"cds_length": 277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000522094.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"hgvs_c": "n.392C>T",
"hgvs_p": null,
"transcript": "ENST00000517936.1",
"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": "ENST00000517936.1"
}
],
"gene_symbol": "HMMR",
"gene_hgnc_id": 5012,
"dbsnp": "rs760286148",
"frequency_reference_population": 6.850197e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8502e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12685862183570862,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.057,
"revel_prediction": "Benign",
"alphamissense_score": 0.1615,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.469,
"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": 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_001142556.2",
"gene_symbol": "HMMR",
"hgnc_id": 5012,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.407C>T",
"hgvs_p": "p.Thr136Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}