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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: 10-97430996-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=97430996&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 97430996,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_002629.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.456C>T",
"hgvs_p": "p.Ser152Ser",
"transcript": "NM_002629.4",
"protein_id": "NP_002620.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 254,
"cds_start": 456,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000334828.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002629.4"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.456C>T",
"hgvs_p": "p.Ser152Ser",
"transcript": "ENST00000334828.6",
"protein_id": "ENSP00000359991.4",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 254,
"cds_start": 456,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002629.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334828.6"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.456C>T",
"hgvs_p": "p.Ser152Ser",
"transcript": "ENST00000889728.1",
"protein_id": "ENSP00000559787.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 250,
"cds_start": 456,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889728.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.420C>T",
"hgvs_p": "p.Ser140Ser",
"transcript": "ENST00000889729.1",
"protein_id": "ENSP00000559788.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 242,
"cds_start": 420,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889729.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.411C>T",
"hgvs_p": "p.Ser137Ser",
"transcript": "NM_001317079.2",
"protein_id": "NP_001304008.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 239,
"cds_start": 411,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317079.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.285C>T",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000940114.1",
"protein_id": "ENSP00000610173.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 197,
"cds_start": 285,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940114.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.415-16C>T",
"hgvs_p": null,
"transcript": "ENST00000940113.1",
"protein_id": "ENSP00000610172.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 235,
"cds_start": null,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940113.1"
},
{
"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": 8,
"intron_rank_end": null,
"gene_symbol": "EXOSC1",
"gene_hgnc_id": 17286,
"hgvs_c": "c.*29-2831G>A",
"hgvs_p": null,
"transcript": "ENST00000889436.1",
"protein_id": "ENSP00000559495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": null,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889436.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "c.140-1359C>T",
"hgvs_p": null,
"transcript": "ENST00000889730.1",
"protein_id": "ENSP00000559789.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": null,
"cds_end": null,
"cds_length": 309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889730.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"hgvs_c": "n.712C>T",
"hgvs_p": null,
"transcript": "ENST00000467867.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000467867.1"
}
],
"gene_symbol": "PGAM1",
"gene_hgnc_id": 8888,
"dbsnp": "rs141766981",
"frequency_reference_population": 0.0003203325,
"hom_count_reference_population": 0,
"allele_count_reference_population": 517,
"gnomad_exomes_af": 0.000181984,
"gnomad_genomes_af": 0.00164828,
"gnomad_exomes_ac": 266,
"gnomad_genomes_ac": 251,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3100000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.237,
"phylop100way_prediction": "Benign",
"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": -15,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 15,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002629.4",
"gene_symbol": "PGAM1",
"hgnc_id": 8888,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.456C>T",
"hgvs_p": "p.Ser152Ser"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000889436.1",
"gene_symbol": "EXOSC1",
"hgnc_id": 17286,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*29-2831G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}