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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: 3-57198246-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57198246&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 57198246,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003865.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "NM_003865.3",
"protein_id": "NP_003856.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295934.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003865.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "ENST00000295934.8",
"protein_id": "ENSP00000295934.3",
"transcript_support_level": 1,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003865.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295934.8"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Ser177Leu",
"transcript": "ENST00000918124.1",
"protein_id": "ENSP00000588183.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 192,
"cds_start": 530,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918124.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "NM_001376058.1",
"protein_id": "NP_001362987.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001376058.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "NM_001376059.1",
"protein_id": "NP_001362988.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001376059.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "NM_001376060.1",
"protein_id": "NP_001362989.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001376060.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "NM_001376061.1",
"protein_id": "NP_001362990.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001376061.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "ENST00000647958.1",
"protein_id": "ENSP00000498190.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647958.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.407C>T",
"hgvs_p": "p.Ser136Leu",
"transcript": "ENST00000473921.2",
"protein_id": "ENSP00000418918.1",
"transcript_support_level": 5,
"aa_start": 136,
"aa_end": null,
"aa_length": 151,
"cds_start": 407,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000473921.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "XM_005265526.5",
"protein_id": "XP_005265583.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265526.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "XM_047449142.1",
"protein_id": "XP_047305098.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449142.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu",
"transcript": "XM_047449143.1",
"protein_id": "XP_047305099.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449143.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "HESX1",
"gene_hgnc_id": 4877,
"hgvs_c": "n.1002C>T",
"hgvs_p": null,
"transcript": "NR_164757.1",
"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": "NR_164757.1"
}
],
"gene_symbol": "HESX1",
"gene_hgnc_id": 4877,
"dbsnp": "rs28936703",
"frequency_reference_population": 0.000060751234,
"hom_count_reference_population": 0,
"allele_count_reference_population": 98,
"gnomad_exomes_af": 0.0000657094,
"gnomad_genomes_af": 0.0000131442,
"gnomad_exomes_ac": 96,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6678951978683472,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.724,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1995,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.801,
"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": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_003865.3",
"gene_symbol": "HESX1",
"hgnc_id": 4877,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Ser170Leu"
}
],
"clinvar_disease": " MILD,GROWTH HORMONE DEFICIENCY WITH PITUITARY ANOMALIES,HESX1-related disorder,SEPTOOPTIC DYSPLASIA,Septo-optic dysplasia sequence,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "SEPTOOPTIC DYSPLASIA, MILD|not provided|GROWTH HORMONE DEFICIENCY WITH PITUITARY ANOMALIES;Septo-optic dysplasia sequence|HESX1-related disorder|Septo-optic dysplasia sequence",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}