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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: 5-16670607-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=16670607&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 16670607,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_012334.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.5802G>T",
"hgvs_p": "p.Met1934Ile",
"transcript": "NM_012334.3",
"protein_id": "NP_036466.2",
"transcript_support_level": null,
"aa_start": 1934,
"aa_end": null,
"aa_length": 2058,
"cds_start": 5802,
"cds_end": null,
"cds_length": 6177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000513610.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012334.3"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.5802G>T",
"hgvs_p": "p.Met1934Ile",
"transcript": "ENST00000513610.6",
"protein_id": "ENSP00000421280.1",
"transcript_support_level": 1,
"aa_start": 1934,
"aa_end": null,
"aa_length": 2058,
"cds_start": 5802,
"cds_end": null,
"cds_length": 6177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012334.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513610.6"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.5835G>T",
"hgvs_p": "p.Met1945Ile",
"transcript": "ENST00000274203.13",
"protein_id": "ENSP00000274203.10",
"transcript_support_level": 5,
"aa_start": 1945,
"aa_end": null,
"aa_length": 2069,
"cds_start": 5835,
"cds_end": null,
"cds_length": 6210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274203.13"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.3819G>T",
"hgvs_p": "p.Met1273Ile",
"transcript": "ENST00000505695.5",
"protein_id": "ENSP00000421170.1",
"transcript_support_level": 2,
"aa_start": 1273,
"aa_end": null,
"aa_length": 1397,
"cds_start": 3819,
"cds_end": null,
"cds_length": 4194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505695.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.3819G>T",
"hgvs_p": "p.Met1273Ile",
"transcript": "ENST00000515803.5",
"protein_id": "ENSP00000425051.1",
"transcript_support_level": 2,
"aa_start": 1273,
"aa_end": null,
"aa_length": 1397,
"cds_start": 3819,
"cds_end": null,
"cds_length": 4194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515803.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.5733G>T",
"hgvs_p": "p.Met1911Ile",
"transcript": "XM_006714475.4",
"protein_id": "XP_006714538.1",
"transcript_support_level": null,
"aa_start": 1911,
"aa_end": null,
"aa_length": 2035,
"cds_start": 5733,
"cds_end": null,
"cds_length": 6108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006714475.4"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.3876G>T",
"hgvs_p": "p.Met1292Ile",
"transcript": "XM_005248306.5",
"protein_id": "XP_005248363.1",
"transcript_support_level": null,
"aa_start": 1292,
"aa_end": null,
"aa_length": 1416,
"cds_start": 3876,
"cds_end": null,
"cds_length": 4251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248306.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.3873G>T",
"hgvs_p": "p.Met1291Ile",
"transcript": "XM_005248307.3",
"protein_id": "XP_005248364.1",
"transcript_support_level": null,
"aa_start": 1291,
"aa_end": null,
"aa_length": 1415,
"cds_start": 3873,
"cds_end": null,
"cds_length": 4248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248307.3"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"hgvs_c": "c.3873G>T",
"hgvs_p": "p.Met1291Ile",
"transcript": "XM_011514046.3",
"protein_id": "XP_011512348.1",
"transcript_support_level": null,
"aa_start": 1291,
"aa_end": null,
"aa_length": 1415,
"cds_start": 3873,
"cds_end": null,
"cds_length": 4248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514046.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RETREG1-AS1",
"gene_hgnc_id": 55551,
"hgvs_c": "n.330-8227C>A",
"hgvs_p": null,
"transcript": "ENST00000653650.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000653650.1"
}
],
"gene_symbol": "MYO10",
"gene_hgnc_id": 7593,
"dbsnp": "rs753290235",
"frequency_reference_population": 0.00000433733,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.0000041048,
"gnomad_genomes_af": 0.00000657056,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28065013885498047,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.317,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4113,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.088,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_012334.3",
"gene_symbol": "MYO10",
"hgnc_id": 7593,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5802G>T",
"hgvs_p": "p.Met1934Ile"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000653650.1",
"gene_symbol": "RETREG1-AS1",
"hgnc_id": 55551,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.330-8227C>A",
"hgvs_p": null
}
],
"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
}