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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: 4-155929695-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=155929695&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 155929695,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001334.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "NM_001334.3",
"protein_id": "NP_001325.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 321,
"cds_start": 685,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000433477.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001334.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000433477.4",
"protein_id": "ENSP00000414904.3",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 321,
"cds_start": 685,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001334.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433477.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"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": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000679996.1",
"protein_id": "ENSP00000505550.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 333,
"cds_start": 685,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679996.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000680741.1",
"protein_id": "ENSP00000505756.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 320,
"cds_start": 685,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680741.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000859966.1",
"protein_id": "ENSP00000530025.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 318,
"cds_start": 685,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859966.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000680553.1",
"protein_id": "ENSP00000505290.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 313,
"cds_start": 685,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680553.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Asp204Asn",
"transcript": "ENST00000859967.1",
"protein_id": "ENSP00000530026.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 296,
"cds_start": 610,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859967.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000679136.1",
"protein_id": "ENSP00000503875.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 295,
"cds_start": 685,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679136.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn",
"transcript": "ENST00000679942.1",
"protein_id": "ENSP00000506416.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 290,
"cds_start": 685,
"cds_end": null,
"cds_length": 873,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679942.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Asp173Asn",
"transcript": "ENST00000952268.1",
"protein_id": "ENSP00000622327.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 265,
"cds_start": 517,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952268.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.685G>A",
"hgvs_p": null,
"transcript": "ENST00000676791.2",
"protein_id": "ENSP00000504976.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000676791.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*539G>A",
"hgvs_p": null,
"transcript": "ENST00000678374.1",
"protein_id": "ENSP00000504174.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000678374.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*503G>A",
"hgvs_p": null,
"transcript": "ENST00000679625.1",
"protein_id": "ENSP00000506073.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000679625.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*603G>A",
"hgvs_p": null,
"transcript": "ENST00000681379.1",
"protein_id": "ENSP00000505854.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000681379.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*539G>A",
"hgvs_p": null,
"transcript": "ENST00000678374.1",
"protein_id": "ENSP00000504174.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000678374.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*503G>A",
"hgvs_p": null,
"transcript": "ENST00000679625.1",
"protein_id": "ENSP00000506073.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000679625.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"hgvs_c": "n.*603G>A",
"hgvs_p": null,
"transcript": "ENST00000681379.1",
"protein_id": "ENSP00000505854.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000681379.1"
}
],
"gene_symbol": "CTSO",
"gene_hgnc_id": 2542,
"dbsnp": "rs1334389012",
"frequency_reference_population": 0.0000055981427,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000549649,
"gnomad_genomes_af": 0.00000657022,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2739737629890442,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.061,
"revel_prediction": "Benign",
"alphamissense_score": 0.0727,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.106,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001334.3",
"gene_symbol": "CTSO",
"hgnc_id": 2542,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.685G>A",
"hgvs_p": "p.Asp229Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}