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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: 3-39411688-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39411688&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 39411688,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000301821.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "NM_002295.6",
"protein_id": "NP_002286.2",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1140,
"mane_select": "ENST00000301821.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000301821.11",
"protein_id": "ENSP00000346067.4",
"transcript_support_level": 1,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1140,
"mane_select": "NM_002295.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Trp",
"transcript": "ENST00000443003.2",
"protein_id": "ENSP00000389351.1",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 300,
"cds_start": 553,
"cds_end": null,
"cds_length": 903,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1032,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.2478C>T",
"hgvs_p": null,
"transcript": "ENST00000495394.2",
"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": 3110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Trp",
"transcript": "NM_001304288.2",
"protein_id": "NP_001291217.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 300,
"cds_start": 553,
"cds_end": null,
"cds_length": 903,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 1155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000458478.6",
"protein_id": "ENSP00000410848.2",
"transcript_support_level": 2,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 621,
"cdna_end": null,
"cdna_length": 1041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000697729.1",
"protein_id": "ENSP00000513423.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 1060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000697730.1",
"protein_id": "ENSP00000513424.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 1158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000697731.1",
"protein_id": "ENSP00000513425.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 295,
"cds_start": 538,
"cds_end": null,
"cds_length": 888,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 1079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp",
"transcript": "ENST00000697728.1",
"protein_id": "ENSP00000513422.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 274,
"cds_start": 538,
"cds_end": null,
"cds_length": 825,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "c.235C>T",
"hgvs_p": "p.Arg79Trp",
"transcript": "ENST00000697754.1",
"protein_id": "ENSP00000513433.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 193,
"cds_start": 235,
"cds_end": null,
"cds_length": 582,
"cdna_start": 237,
"cdna_end": null,
"cdna_length": 654,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.1088C>T",
"hgvs_p": null,
"transcript": "ENST00000478027.3",
"protein_id": null,
"transcript_support_level": 2,
"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": 1508,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.1175C>T",
"hgvs_p": null,
"transcript": "ENST00000697732.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1247,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.1823C>T",
"hgvs_p": null,
"transcript": "ENST00000697733.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2431,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.2471C>T",
"hgvs_p": null,
"transcript": "ENST00000697734.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2856,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.1821C>T",
"hgvs_p": null,
"transcript": "ENST00000697735.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2225,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.538C>T",
"hgvs_p": null,
"transcript": "ENST00000697753.1",
"protein_id": "ENSP00000513432.1",
"transcript_support_level": null,
"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": 3593,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.*435C>T",
"hgvs_p": null,
"transcript": "ENST00000697816.1",
"protein_id": "ENSP00000513451.1",
"transcript_support_level": null,
"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": 1070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"hgvs_c": "n.*435C>T",
"hgvs_p": null,
"transcript": "ENST00000697816.1",
"protein_id": "ENSP00000513451.1",
"transcript_support_level": null,
"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": 1070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPSA",
"gene_hgnc_id": 6502,
"dbsnp": "rs397514760",
"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": 0.8342050313949585,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.301,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9957,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.571,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000301821.11",
"gene_symbol": "RPSA",
"hgnc_id": 6502,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.538C>T",
"hgvs_p": "p.Arg180Trp"
}
],
"clinvar_disease": "Familial isolated congenital asplenia,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Familial isolated congenital asplenia|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}