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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: 6-131583862-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131583862&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ARG1",
"hgnc_id": 663,
"hgvs_c": "c.947G>A",
"hgvs_p": "p.Arg316Gln",
"inheritance_mode": "AR",
"pathogenic_score": 14,
"score": 14,
"transcript": "NM_001244438.2",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MED23",
"hgnc_id": 2372,
"hgvs_c": "c.4095+3847C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_015979.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 14,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.7741,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.51,
"chr": "6",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Arginase deficiency",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8685786724090576,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 322,
"aa_ref": "R",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1447,
"cdna_start": 980,
"cds_end": null,
"cds_length": 969,
"cds_start": 923,
"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.923G>A",
"hgvs_p": "p.Arg308Gln",
"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": "Q",
"aa_end": null,
"aa_length": 322,
"aa_ref": "R",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1447,
"cdna_start": 980,
"cds_end": null,
"cds_length": 969,
"cds_start": 923,
"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.923G>A",
"hgvs_p": "p.Arg308Gln",
"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": "Q",
"aa_end": null,
"aa_length": 330,
"aa_ref": "R",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1468,
"cdna_start": 1005,
"cds_end": null,
"cds_length": 993,
"cds_start": 947,
"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.947G>A",
"hgvs_p": "p.Arg316Gln",
"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+3847C>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": "Q",
"aa_end": null,
"aa_length": 330,
"aa_ref": "R",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1471,
"cdna_start": 1004,
"cds_end": null,
"cds_length": 993,
"cds_start": 947,
"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.947G>A",
"hgvs_p": "p.Arg316Gln",
"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": "Q",
"aa_end": null,
"aa_length": 318,
"aa_ref": "R",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1425,
"cdna_start": 965,
"cds_end": null,
"cds_length": 957,
"cds_start": 911,
"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.911G>A",
"hgvs_p": "p.Arg304Gln",
"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": "Q",
"aa_end": null,
"aa_length": 311,
"aa_ref": "R",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1405,
"cdna_start": 945,
"cds_end": null,
"cds_length": 936,
"cds_start": 890,
"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.890G>A",
"hgvs_p": "p.Arg297Gln",
"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": "Q",
"aa_end": null,
"aa_length": 304,
"aa_ref": "R",
"aa_start": 290,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1059,
"cdna_start": 943,
"cds_end": null,
"cds_length": 915,
"cds_start": 869,
"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.869G>A",
"hgvs_p": "p.Arg290Gln",
"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": "Q",
"aa_end": null,
"aa_length": 297,
"aa_ref": "R",
"aa_start": 283,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1362,
"cdna_start": 902,
"cds_end": null,
"cds_length": 894,
"cds_start": 848,
"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.848G>A",
"hgvs_p": "p.Arg283Gln",
"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": "Q",
"aa_end": null,
"aa_length": 294,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1353,
"cdna_start": 893,
"cds_end": null,
"cds_length": 885,
"cds_start": 839,
"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.839G>A",
"hgvs_p": "p.Arg280Gln",
"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": "Q",
"aa_end": null,
"aa_length": 287,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1368,
"cdna_start": 899,
"cds_end": null,
"cds_length": 864,
"cds_start": 818,
"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.818G>A",
"hgvs_p": "p.Arg273Gln",
"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": "Q",
"aa_end": null,
"aa_length": 237,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1192,
"cdna_start": 725,
"cds_end": null,
"cds_length": 714,
"cds_start": 668,
"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.668G>A",
"hgvs_p": "p.Arg223Gln",
"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": "Q",
"aa_end": null,
"aa_length": 237,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1192,
"cdna_start": 722,
"cds_end": null,
"cds_length": 714,
"cds_start": 668,
"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.668G>A",
"hgvs_p": "p.Arg223Gln",
"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": "Q",
"aa_end": null,
"aa_length": 202,
"aa_ref": "R",
"aa_start": 188,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1080,
"cdna_start": 620,
"cds_end": null,
"cds_length": 609,
"cds_start": 563,
"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.563G>A",
"hgvs_p": "p.Arg188Gln",
"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": "Q",
"aa_end": null,
"aa_length": 186,
"aa_ref": "R",
"aa_start": 172,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1029,
"cdna_start": 569,
"cds_end": null,
"cds_length": 561,
"cds_start": 515,
"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.515G>A",
"hgvs_p": "p.Arg172Gln",
"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+3847C>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+3847C>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.*810G>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.907G>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.*810G>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": "rs377280518",
"effect": "missense_variant",
"frequency_reference_population": 0.000008674209,
"gene_hgnc_id": 663,
"gene_symbol": "ARG1",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000752491,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197151,
"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": "Pathogenic",
"phenotype_combined": "Arginase deficiency",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.082,
"pos": 131583862,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.825,
"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"
}
]
}