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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: 17-3476238-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3476238&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 3476238,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000263080.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "NM_000049.4",
"protein_id": "NP_000040.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 313,
"cds_start": 79,
"cds_end": null,
"cds_length": 942,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 5422,
"mane_select": "ENST00000263080.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "ENST00000263080.3",
"protein_id": "ENSP00000263080.2",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 313,
"cds_start": 79,
"cds_end": null,
"cds_length": 942,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 5422,
"mane_select": "NM_000049.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "ENST00000456349.6",
"protein_id": "ENSP00000409976.2",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 313,
"cds_start": 79,
"cds_end": null,
"cds_length": 942,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 1090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "NM_001128085.1",
"protein_id": "NP_001121557.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 313,
"cds_start": 79,
"cds_end": null,
"cds_length": 942,
"cdna_start": 170,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "ENST00000577034.1",
"protein_id": "ENSP00000458324.1",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 77,
"cds_start": 79,
"cds_end": null,
"cds_length": 236,
"cdna_start": 406,
"cdna_end": null,
"cdna_length": 563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg",
"transcript": "XM_017024661.2",
"protein_id": "XP_016880150.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 313,
"cds_start": 79,
"cds_end": null,
"cds_length": 942,
"cdna_start": 382,
"cdna_end": null,
"cdna_length": 5562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"hgvs_c": "n.79G>A",
"hgvs_p": null,
"transcript": "ENST00000571278.1",
"protein_id": "ENSP00000461358.1",
"transcript_support_level": 5,
"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": 584,
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA22",
"gene_hgnc_id": 30705,
"hgvs_c": "c.-73-6840C>T",
"hgvs_p": null,
"transcript": "NM_001321337.2",
"protein_id": "NP_001308266.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 363,
"cds_start": -4,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1740,
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA22",
"gene_hgnc_id": 30705,
"hgvs_c": "c.-73-6840C>T",
"hgvs_p": null,
"transcript": "NM_001321336.2",
"protein_id": "NP_001308265.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 347,
"cds_start": -4,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1692,
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA22",
"gene_hgnc_id": 30705,
"hgvs_c": "c.-73-6840C>T",
"hgvs_p": null,
"transcript": "ENST00000541913.5",
"protein_id": "ENSP00000441920.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 347,
"cds_start": -4,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1683,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA22",
"gene_hgnc_id": 30705,
"hgvs_c": "c.-73-6840C>T",
"hgvs_p": null,
"transcript": "ENST00000570318.1",
"protein_id": "ENSP00000459147.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 2,
"cds_start": -4,
"cds_end": null,
"cds_length": 9,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ASPA",
"gene_hgnc_id": 756,
"dbsnp": "rs766328537",
"frequency_reference_population": 0.000016728438,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000150496,
"gnomad_genomes_af": 0.000032855,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9930398464202881,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.977,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9708,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.723,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000263080.3",
"gene_symbol": "ASPA",
"hgnc_id": 756,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.79G>A",
"hgvs_p": "p.Gly27Arg"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001321337.2",
"gene_symbol": "SPATA22",
"hgnc_id": 30705,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-73-6840C>T",
"hgvs_p": null
}
],
"clinvar_disease": " Familial Form,Canavan Disease,Spongy degeneration of central nervous system,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1",
"phenotype_combined": "Spongy degeneration of central nervous system|not provided|Canavan Disease, Familial Form",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}