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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: 3-196241987-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196241987&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196241987,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000431016.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "NM_001312673.2",
"protein_id": "NP_001299602.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 791,
"cdna_end": null,
"cdna_length": 5546,
"mane_select": "ENST00000431016.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "ENST00000431016.6",
"protein_id": "ENSP00000394617.1",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 791,
"cdna_end": null,
"cdna_length": 5546,
"mane_select": "NM_001312673.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "ENST00000292823.6",
"protein_id": "ENSP00000292823.2",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 842,
"cdna_end": null,
"cdna_length": 5597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "ENST00000419333.5",
"protein_id": "ENSP00000390968.1",
"transcript_support_level": 5,
"aa_start": 223,
"aa_end": null,
"aa_length": 380,
"cds_start": 669,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 1325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "NM_005017.4",
"protein_id": "NP_005008.2",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 5610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser",
"transcript": "ENST00000411591.5",
"protein_id": "ENSP00000400430.1",
"transcript_support_level": 3,
"aa_start": 223,
"aa_end": null,
"aa_length": 292,
"cds_start": 669,
"cds_end": null,
"cds_length": 879,
"cdna_start": 874,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"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": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.471G>C",
"hgvs_p": "p.Arg157Ser",
"transcript": "ENST00000430755.5",
"protein_id": "ENSP00000402283.1",
"transcript_support_level": 3,
"aa_start": 157,
"aa_end": null,
"aa_length": 201,
"cds_start": 471,
"cds_end": null,
"cds_length": 606,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.288G>C",
"hgvs_p": "p.Arg96Ser",
"transcript": "ENST00000433733.5",
"protein_id": "ENSP00000390458.1",
"transcript_support_level": 5,
"aa_start": 96,
"aa_end": null,
"aa_length": 136,
"cds_start": 288,
"cds_end": null,
"cds_length": 411,
"cdna_start": 288,
"cdna_end": null,
"cdna_length": 411,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.486+5380G>C",
"hgvs_p": null,
"transcript": "ENST00000441879.5",
"protein_id": "ENSP00000392397.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": -4,
"cds_end": null,
"cds_length": 638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.58-507C>G",
"hgvs_p": null,
"transcript": "ENST00000415111.1",
"protein_id": "ENSP00000409560.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 23,
"cds_start": -4,
"cds_end": null,
"cds_length": 72,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.*80G>C",
"hgvs_p": null,
"transcript": "ENST00000473978.5",
"protein_id": null,
"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": 1430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"dbsnp": "rs540053239",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7817221879959106,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.694,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9997,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.107,
"phylop100way_prediction": "Benign",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000431016.6",
"gene_symbol": "PCYT1A",
"hgnc_id": 8754,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.669G>C",
"hgvs_p": "p.Arg223Ser"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000415111.1",
"gene_symbol": "SLC51A",
"hgnc_id": 29955,
"effects": [
"intron_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.58-507C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}