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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: 17-58495011-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58495011&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 58495011,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001378067.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3173G>A",
"hgvs_p": "p.Arg1058His",
"transcript": "NM_001378067.1",
"protein_id": "NP_001364996.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1209,
"cds_start": 3173,
"cds_end": null,
"cds_length": 3630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000682306.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378067.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3173G>A",
"hgvs_p": "p.Arg1058His",
"transcript": "ENST00000682306.1",
"protein_id": "ENSP00000507664.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1209,
"cds_start": 3173,
"cds_end": null,
"cds_length": 3630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001378067.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682306.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3131G>A",
"hgvs_p": "p.Arg1044His",
"transcript": "ENST00000323456.9",
"protein_id": "ENSP00000325285.5",
"transcript_support_level": 1,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323456.9"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3269G>A",
"hgvs_p": "p.Arg1090His",
"transcript": "ENST00000955804.1",
"protein_id": "ENSP00000625863.1",
"transcript_support_level": null,
"aa_start": 1090,
"aa_end": null,
"aa_length": 1241,
"cds_start": 3269,
"cds_end": null,
"cds_length": 3726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955804.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3143G>A",
"hgvs_p": "p.Arg1048His",
"transcript": "NM_001378066.1",
"protein_id": "NP_001364995.1",
"transcript_support_level": null,
"aa_start": 1048,
"aa_end": null,
"aa_length": 1199,
"cds_start": 3143,
"cds_end": null,
"cds_length": 3600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378066.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3131G>A",
"hgvs_p": "p.Arg1044His",
"transcript": "NM_004687.5",
"protein_id": "NP_004678.3",
"transcript_support_level": null,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004687.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3056G>A",
"hgvs_p": "p.Arg1019His",
"transcript": "ENST00000938934.1",
"protein_id": "ENSP00000608993.1",
"transcript_support_level": null,
"aa_start": 1019,
"aa_end": null,
"aa_length": 1170,
"cds_start": 3056,
"cds_end": null,
"cds_length": 3513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938934.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.2960G>A",
"hgvs_p": "p.Arg987His",
"transcript": "ENST00000579925.5",
"protein_id": "ENSP00000464067.1",
"transcript_support_level": 5,
"aa_start": 987,
"aa_end": null,
"aa_length": 1138,
"cds_start": 2960,
"cds_end": null,
"cds_length": 3417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000579925.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3143G>A",
"hgvs_p": "p.Arg1048His",
"transcript": "XM_011525460.4",
"protein_id": "XP_011523762.1",
"transcript_support_level": null,
"aa_start": 1048,
"aa_end": null,
"aa_length": 1199,
"cds_start": 3143,
"cds_end": null,
"cds_length": 3600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525460.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3131G>A",
"hgvs_p": "p.Arg1044His",
"transcript": "XM_005257786.6",
"protein_id": "XP_005257843.1",
"transcript_support_level": null,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005257786.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3131G>A",
"hgvs_p": "p.Arg1044His",
"transcript": "XM_006722168.5",
"protein_id": "XP_006722231.1",
"transcript_support_level": null,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722168.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"hgvs_c": "c.3131G>A",
"hgvs_p": "p.Arg1044His",
"transcript": "XM_047437019.1",
"protein_id": "XP_047292975.1",
"transcript_support_level": null,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437019.1"
}
],
"gene_symbol": "MTMR4",
"gene_hgnc_id": 7452,
"dbsnp": "rs774894520",
"frequency_reference_population": 0.000027257578,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000191532,
"gnomad_genomes_af": 0.000105031,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1698094606399536,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.384,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1457,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.634,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001378067.1",
"gene_symbol": "MTMR4",
"hgnc_id": 7452,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3173G>A",
"hgvs_p": "p.Arg1058His"
}
],
"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
}