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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: 3-49721758-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49721758&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49721758,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000308388.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1077C>G",
"hgvs_p": "p.Ile359Met",
"transcript": "NM_021971.4",
"protein_id": "NP_068806.2",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 360,
"cds_start": 1077,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 3144,
"mane_select": "ENST00000308388.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1077C>G",
"hgvs_p": "p.Ile359Met",
"transcript": "ENST00000308388.7",
"protein_id": "ENSP00000311130.6",
"transcript_support_level": 1,
"aa_start": 359,
"aa_end": null,
"aa_length": 360,
"cds_start": 1077,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 3144,
"mane_select": "NM_021971.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1185C>G",
"hgvs_p": "p.Ile395Met",
"transcript": "ENST00000495627.2",
"protein_id": "ENSP00000503768.1",
"transcript_support_level": 2,
"aa_start": 395,
"aa_end": null,
"aa_length": 396,
"cds_start": 1185,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 1660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1158C>G",
"hgvs_p": "p.Ile386Met",
"transcript": "NM_013334.4",
"protein_id": "NP_037466.3",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 387,
"cds_start": 1158,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1383,
"cdna_end": null,
"cdna_length": 1642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1158C>G",
"hgvs_p": "p.Ile386Met",
"transcript": "ENST00000308375.10",
"protein_id": "ENSP00000309092.6",
"transcript_support_level": 2,
"aa_start": 386,
"aa_end": null,
"aa_length": 387,
"cds_start": 1158,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1383,
"cdna_end": null,
"cdna_length": 3217,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.1077C>G",
"hgvs_p": "p.Ile359Met",
"transcript": "ENST00000480687.5",
"protein_id": "ENSP00000418565.1",
"transcript_support_level": 2,
"aa_start": 359,
"aa_end": null,
"aa_length": 360,
"cds_start": 1077,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 6108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000678010.1",
"protein_id": "ENSP00000503176.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 238,
"cds_start": 711,
"cds_end": null,
"cds_length": 717,
"cdna_start": 906,
"cdna_end": null,
"cdna_length": 2048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "n.1650C>G",
"hgvs_p": null,
"transcript": "ENST00000481959.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "n.1511C>G",
"hgvs_p": null,
"transcript": "ENST00000678208.1",
"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": 2919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "n.*368C>G",
"hgvs_p": null,
"transcript": "ENST00000678853.1",
"protein_id": "ENSP00000504692.1",
"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": 2389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "c.*94C>G",
"hgvs_p": null,
"transcript": "ENST00000677393.1",
"protein_id": "ENSP00000503880.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": -4,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"hgvs_c": "n.*368C>G",
"hgvs_p": null,
"transcript": "ENST00000678853.1",
"protein_id": "ENSP00000504692.1",
"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": 2389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "c.*453G>C",
"hgvs_p": null,
"transcript": "NM_022064.5",
"protein_id": "NP_071347.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1314,
"cds_start": -4,
"cds_end": null,
"cds_length": 3945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4255,
"mane_select": "ENST00000327697.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "c.*453G>C",
"hgvs_p": null,
"transcript": "ENST00000327697.11",
"protein_id": "ENSP00000328287.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1314,
"cds_start": -4,
"cds_end": null,
"cds_length": 3945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4255,
"mane_select": "NM_022064.5",
"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": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "n.*2472G>C",
"hgvs_p": null,
"transcript": "ENST00000457726.5",
"protein_id": "ENSP00000394369.1",
"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": 4506,
"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": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "n.*229G>C",
"hgvs_p": null,
"transcript": "ENST00000486102.5",
"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": 4564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "c.*453G>C",
"hgvs_p": null,
"transcript": "ENST00000433785.1",
"protein_id": "ENSP00000416156.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 426,
"cds_start": -4,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1555,
"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": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "n.*231G>C",
"hgvs_p": null,
"transcript": "ENST00000487805.6",
"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": 5882,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "n.*229G>C",
"hgvs_p": null,
"transcript": "ENST00000498376.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 746,
"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": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF123",
"gene_hgnc_id": 21148,
"hgvs_c": "n.*229G>C",
"hgvs_p": null,
"transcript": "NR_135218.2",
"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": 4495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GMPPB",
"gene_hgnc_id": 22932,
"dbsnp": "rs1553691662",
"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": 0.8330333232879639,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.625,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5902,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.984,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000308388.7",
"gene_symbol": "GMPPB",
"hgnc_id": 22932,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1077C>G",
"hgvs_p": "p.Ile359Met"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000327697.11",
"gene_symbol": "RNF123",
"hgnc_id": 21148,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*453G>C",
"hgvs_p": null
}
],
"clinvar_disease": " type A14, type B14,Autosomal recessive limb-girdle muscular dystrophy type 2T,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability)",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14;Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14;Autosomal recessive limb-girdle muscular dystrophy type 2T",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}