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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: 3-63615323-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=63615323&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SYNPR",
"hgnc_id": 16507,
"hgvs_c": "c.700C>T",
"hgvs_p": "p.Pro234Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001130003.2",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SYNPR-AS1",
"hgnc_id": 40774,
"hgvs_c": "n.123+30192G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000803954.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.0647,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.03429955244064331,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 285,
"aa_ref": "P",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2527,
"cdna_start": 926,
"cds_end": null,
"cds_length": 858,
"cds_start": 700,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001130003.2",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.700C>T",
"hgvs_p": "p.Pro234Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000478300.6",
"protein_coding": true,
"protein_id": "NP_001123475.1",
"strand": true,
"transcript": "NM_001130003.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 285,
"aa_ref": "P",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2527,
"cdna_start": 926,
"cds_end": null,
"cds_length": 858,
"cds_start": 700,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000478300.6",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.700C>T",
"hgvs_p": "p.Pro234Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001130003.2",
"protein_coding": true,
"protein_id": "ENSP00000418994.1",
"strand": true,
"transcript": "ENST00000478300.6",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 265,
"aa_ref": "P",
"aa_start": 214,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2607,
"cdna_start": 1009,
"cds_end": null,
"cds_length": 798,
"cds_start": 640,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000295894.9",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.640C>T",
"hgvs_p": "p.Pro214Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000295894.5",
"strand": true,
"transcript": "ENST00000295894.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 34,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1004,
"cdna_start": null,
"cds_end": null,
"cds_length": 105,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000450542.6",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.*470C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402121.2",
"strand": true,
"transcript": "ENST00000450542.6",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 276,
"aa_ref": "P",
"aa_start": 225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2383,
"cdna_start": 786,
"cds_end": null,
"cds_length": 831,
"cds_start": 673,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000460711.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418701.1",
"strand": true,
"transcript": "ENST00000460711.5",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 265,
"aa_ref": "P",
"aa_start": 214,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2375,
"cdna_start": 774,
"cds_end": null,
"cds_length": 798,
"cds_start": 640,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_144642.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.640C>T",
"hgvs_p": "p.Pro214Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_653243.1",
"strand": true,
"transcript": "NM_144642.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 829,
"cdna_start": 557,
"cds_end": null,
"cds_length": 606,
"cds_start": 448,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000465156.1",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.448C>T",
"hgvs_p": "p.Pro150Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418123.1",
"strand": true,
"transcript": "ENST00000465156.1",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 301,
"aa_ref": "P",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2363,
"cdna_start": 762,
"cds_end": null,
"cds_length": 906,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017005731.1",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.748C>T",
"hgvs_p": "p.Pro250Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861220.1",
"strand": true,
"transcript": "XM_017005731.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 202,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2436,
"cdna_start": null,
"cds_end": null,
"cds_length": 609,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000479198.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.*111C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418929.1",
"strand": true,
"transcript": "ENST00000479198.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1304,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000468110.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "n.*273C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419441.1",
"strand": true,
"transcript": "ENST00000468110.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1296,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000498449.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "n.*273C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420383.1",
"strand": true,
"transcript": "ENST00000498449.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1304,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000468110.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "n.*273C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419441.1",
"strand": true,
"transcript": "ENST00000468110.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1296,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000498449.5",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "n.*273C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420383.1",
"strand": true,
"transcript": "ENST00000498449.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2784,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000803954.1",
"gene_hgnc_id": 40774,
"gene_symbol": "SYNPR-AS1",
"hgvs_c": "n.123+30192G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000803954.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 927,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000803955.1",
"gene_hgnc_id": 40774,
"gene_symbol": "SYNPR-AS1",
"hgvs_c": "n.74+30192G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000803955.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 254,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000803956.1",
"gene_hgnc_id": 40774,
"gene_symbol": "SYNPR-AS1",
"hgvs_c": "n.80+30192G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000803956.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 222,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5527,
"cdna_start": null,
"cds_end": null,
"cds_length": 669,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017005732.3",
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"hgvs_c": "c.*4781C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861221.1",
"strand": true,
"transcript": "XM_017005732.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs755131264",
"effect": "missense_variant",
"frequency_reference_population": 0.0000018591093,
"gene_hgnc_id": 16507,
"gene_symbol": "SYNPR",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136834,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065767,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.699,
"pos": 63615323,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.03,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001130003.2"
}
]
}