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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: 12-57498217-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57498217&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57498217,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000262027.10",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.831T>C",
"hgvs_p": "p.Asn277Asn",
"transcript": "NM_004990.4",
"protein_id": "NP_004981.2",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 900,
"cds_start": 831,
"cds_end": null,
"cds_length": 2703,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 2797,
"mane_select": "ENST00000262027.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.831T>C",
"hgvs_p": "p.Asn277Asn",
"transcript": "ENST00000262027.10",
"protein_id": "ENSP00000262027.5",
"transcript_support_level": 1,
"aa_start": 277,
"aa_end": null,
"aa_length": 900,
"cds_start": 831,
"cds_end": null,
"cds_length": 2703,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 2797,
"mane_select": "NM_004990.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.129T>C",
"hgvs_p": "p.Asn43Asn",
"transcript": "XM_047428851.1",
"protein_id": "XP_047284807.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 666,
"cds_start": 129,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 2352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.831T>C",
"hgvs_p": "p.Asn277Asn",
"transcript": "XM_047428852.1",
"protein_id": "XP_047284808.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 546,
"cds_start": 831,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 1728,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.473T>C",
"hgvs_p": null,
"transcript": "ENST00000447721.6",
"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": 1328,
"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": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.831T>C",
"hgvs_p": null,
"transcript": "ENST00000537638.6",
"protein_id": "ENSP00000446168.2",
"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": 3592,
"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": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.*332T>C",
"hgvs_p": null,
"transcript": "ENST00000545888.6",
"protein_id": "ENSP00000439307.2",
"transcript_support_level": 5,
"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": 2979,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.725T>C",
"hgvs_p": null,
"transcript": "ENST00000548674.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 749,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.*196T>C",
"hgvs_p": null,
"transcript": "ENST00000551892.1",
"protein_id": "ENSP00000450018.1",
"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": 748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.*332T>C",
"hgvs_p": null,
"transcript": "ENST00000628866.2",
"protein_id": "ENSP00000486738.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 95,
"cds_start": -4,
"cds_end": null,
"cds_length": 288,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2583,
"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": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.*332T>C",
"hgvs_p": null,
"transcript": "ENST00000545888.6",
"protein_id": "ENSP00000439307.2",
"transcript_support_level": 5,
"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": 2979,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.*196T>C",
"hgvs_p": null,
"transcript": "ENST00000551892.1",
"protein_id": "ENSP00000450018.1",
"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": 748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "c.384-203T>C",
"hgvs_p": null,
"transcript": "ENST00000552371.1",
"protein_id": "ENSP00000447914.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 231,
"cds_start": -4,
"cds_end": null,
"cds_length": 697,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 699,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"hgvs_c": "n.*196T>C",
"hgvs_p": null,
"transcript": "ENST00000549074.5",
"protein_id": "ENSP00000447258.1",
"transcript_support_level": 4,
"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": 532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MARS1",
"gene_hgnc_id": 6898,
"dbsnp": "rs367995771",
"frequency_reference_population": 0.0000136298695,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000116288,
"gnomad_genomes_af": 0.0000328494,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6700000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.269,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000262027.10",
"gene_symbol": "MARS1",
"hgnc_id": 6898,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,AD,AR",
"hgvs_c": "c.831T>C",
"hgvs_p": "p.Asn277Asn"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease axonal type 2U,Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency;Charcot-Marie-Tooth disease axonal type 2U|not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}