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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: 7-155803249-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=155803249&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 155803249,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000193.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.1040C>G",
"hgvs_p": "p.Pro347Arg",
"transcript": "NM_000193.4",
"protein_id": "NP_000184.1",
"transcript_support_level": null,
"aa_start": 347,
"aa_end": null,
"aa_length": 462,
"cds_start": 1040,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 4650,
"mane_select": "ENST00000297261.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.1040C>G",
"hgvs_p": "p.Pro347Arg",
"transcript": "ENST00000297261.7",
"protein_id": "ENSP00000297261.2",
"transcript_support_level": 1,
"aa_start": 347,
"aa_end": null,
"aa_length": 462,
"cds_start": 1040,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 4650,
"mane_select": "NM_000193.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.302-3004C>G",
"hgvs_p": null,
"transcript": "ENST00000430104.5",
"protein_id": "ENSP00000396621.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "n.302-2652C>G",
"hgvs_p": null,
"transcript": "ENST00000435425.1",
"protein_id": "ENSP00000413871.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "n.302-2582C>G",
"hgvs_p": null,
"transcript": "ENST00000441114.5",
"protein_id": "ENSP00000410546.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.779C>G",
"hgvs_p": "p.Pro260Arg",
"transcript": "XM_011516479.3",
"protein_id": "XP_011514781.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 375,
"cds_start": 779,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 1040,
"cdna_end": null,
"cdna_length": 4309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.779C>G",
"hgvs_p": "p.Pro260Arg",
"transcript": "XM_011516480.3",
"protein_id": "XP_011514782.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 375,
"cds_start": 779,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 1338,
"cdna_end": null,
"cdna_length": 4607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.701C>G",
"hgvs_p": "p.Pro234Arg",
"transcript": "XM_047420718.1",
"protein_id": "XP_047276674.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 349,
"cds_start": 701,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 4180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "c.302-3004C>G",
"hgvs_p": null,
"transcript": "NM_001310462.2",
"protein_id": "NP_001297391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "n.563-2582C>G",
"hgvs_p": null,
"transcript": "NR_132318.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"hgvs_c": "n.563-2652C>G",
"hgvs_p": null,
"transcript": "NR_132319.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SHH",
"gene_hgnc_id": 10848,
"dbsnp": "rs886042458",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9944648742675781,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.977,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9914,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.17,
"phylop100way_prediction": "Pathogenic",
"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": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000193.4",
"gene_symbol": "SHH",
"hgnc_id": 10848,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1040C>G",
"hgvs_p": "p.Pro347Arg"
}
],
"clinvar_disease": "Holoprosencephaly 3,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "not provided|Holoprosencephaly 3",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}