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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: 6-131583831-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131583831&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ARG1",
"hgnc_id": 663,
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Ala306Thr",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_001244438.2",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MED23",
"hgnc_id": 2372,
"hgvs_c": "c.4095+3878C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_015979.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5",
"acmg_score": 6,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.1434,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Arginase deficiency",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5855388641357422,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 322,
"aa_ref": "A",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1447,
"cdna_start": 949,
"cds_end": null,
"cds_length": 969,
"cds_start": 892,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_000045.4",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.892G>A",
"hgvs_p": "p.Ala298Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000368087.8",
"protein_coding": true,
"protein_id": "NP_000036.2",
"strand": true,
"transcript": "NM_000045.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 322,
"aa_ref": "A",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1447,
"cdna_start": 949,
"cds_end": null,
"cds_length": 969,
"cds_start": 892,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000368087.8",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.892G>A",
"hgvs_p": "p.Ala298Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000045.4",
"protein_coding": true,
"protein_id": "ENSP00000357066.3",
"strand": true,
"transcript": "ENST00000368087.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 330,
"aa_ref": "A",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1468,
"cdna_start": 974,
"cds_end": null,
"cds_length": 993,
"cds_start": 916,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000356962.2",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Ala306Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349446.2",
"strand": true,
"transcript": "ENST00000356962.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4581,
"cdna_start": null,
"cds_end": null,
"cds_length": 4098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000354577.8",
"gene_hgnc_id": 2372,
"gene_symbol": "MED23",
"hgvs_c": "c.4095+3878C>T",
"hgvs_p": null,
"intron_rank": 30,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000346588.4",
"strand": false,
"transcript": "ENST00000354577.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 330,
"aa_ref": "A",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1471,
"cdna_start": 973,
"cds_end": null,
"cds_length": 993,
"cds_start": 916,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001244438.2",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Ala306Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001231367.1",
"strand": true,
"transcript": "NM_001244438.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 318,
"aa_ref": "A",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1425,
"cdna_start": 934,
"cds_end": null,
"cds_length": 957,
"cds_start": 880,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000875754.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.880G>A",
"hgvs_p": "p.Ala294Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545813.1",
"strand": true,
"transcript": "ENST00000875754.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 311,
"aa_ref": "A",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1405,
"cdna_start": 914,
"cds_end": null,
"cds_length": 936,
"cds_start": 859,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000875752.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.859G>A",
"hgvs_p": "p.Ala287Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545811.1",
"strand": true,
"transcript": "ENST00000875752.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 304,
"aa_ref": "A",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1059,
"cdna_start": 912,
"cds_end": null,
"cds_length": 915,
"cds_start": 838,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000672233.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.838G>A",
"hgvs_p": "p.Ala280Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499826.1",
"strand": true,
"transcript": "ENST00000672233.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 297,
"aa_ref": "A",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1362,
"cdna_start": 871,
"cds_end": null,
"cds_length": 894,
"cds_start": 817,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000875755.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.817G>A",
"hgvs_p": "p.Ala273Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545814.1",
"strand": true,
"transcript": "ENST00000875755.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 294,
"aa_ref": "A",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1353,
"cdna_start": 862,
"cds_end": null,
"cds_length": 885,
"cds_start": 808,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000875753.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Ala270Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545812.1",
"strand": true,
"transcript": "ENST00000875753.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 287,
"aa_ref": "A",
"aa_start": 263,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1368,
"cdna_start": 868,
"cds_end": null,
"cds_length": 864,
"cds_start": 787,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000875750.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Ala263Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545809.1",
"strand": true,
"transcript": "ENST00000875750.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 237,
"aa_ref": "A",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1192,
"cdna_start": 694,
"cds_end": null,
"cds_length": 714,
"cds_start": 637,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001369020.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Ala213Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001355949.1",
"strand": true,
"transcript": "NM_001369020.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 237,
"aa_ref": "A",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1192,
"cdna_start": 691,
"cds_end": null,
"cds_length": 714,
"cds_start": 637,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000673427.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Ala213Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000500160.1",
"strand": true,
"transcript": "ENST00000673427.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 202,
"aa_ref": "A",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1080,
"cdna_start": 589,
"cds_end": null,
"cds_length": 609,
"cds_start": 532,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000875751.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Ala178Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545810.1",
"strand": true,
"transcript": "ENST00000875751.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 186,
"aa_ref": "A",
"aa_start": 162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1029,
"cdna_start": 538,
"cds_end": null,
"cds_length": 561,
"cds_start": 484,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000875756.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Ala162Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545815.1",
"strand": true,
"transcript": "ENST00000875756.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4618,
"cdna_start": null,
"cds_end": null,
"cds_length": 4098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015979.4",
"gene_hgnc_id": 2372,
"gene_symbol": "MED23",
"hgvs_c": "c.4095+3878C>T",
"hgvs_p": null,
"intron_rank": 30,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_057063.2",
"strand": false,
"transcript": "NM_015979.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1359,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4600,
"cdna_start": null,
"cds_end": null,
"cds_length": 4080,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001270521.2",
"gene_hgnc_id": 2372,
"gene_symbol": "MED23",
"hgvs_c": "c.4077+3878C>T",
"hgvs_p": null,
"intron_rank": 29,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001257450.1",
"strand": false,
"transcript": "NM_001270521.2",
"transcript_support_level": null
},
{
"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": 1230,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000673234.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "n.*779G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499885.1",
"strand": true,
"transcript": "ENST00000673234.1",
"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": 1374,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NR_160934.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "n.876G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_160934.1",
"transcript_support_level": null
},
{
"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": 1230,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000673234.1",
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"hgvs_c": "n.*779G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499885.1",
"strand": true,
"transcript": "ENST00000673234.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs755359126",
"effect": "missense_variant",
"frequency_reference_population": 0.0000043370455,
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342041,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131415,
"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": "Arginase deficiency",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.781,
"pos": 131583831,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.292,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001244438.2"
}
]
}