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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: 12-109561103-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=109561103&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 109561103,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000545712.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.521C>T",
"hgvs_p": "p.Ser174Leu",
"transcript": "NM_052845.4",
"protein_id": "NP_443077.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 250,
"cds_start": 521,
"cds_end": null,
"cds_length": 753,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4090,
"mane_select": "ENST00000545712.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.521C>T",
"hgvs_p": "p.Ser174Leu",
"transcript": "ENST00000545712.7",
"protein_id": "ENSP00000445920.1",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 250,
"cds_start": 521,
"cds_end": null,
"cds_length": 753,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4090,
"mane_select": "NM_052845.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.365C>T",
"hgvs_p": "p.Ser122Leu",
"transcript": "ENST00000540016.5",
"protein_id": "ENSP00000474582.1",
"transcript_support_level": 3,
"aa_start": 122,
"aa_end": null,
"aa_length": 198,
"cds_start": 365,
"cds_end": null,
"cds_length": 597,
"cdna_start": 382,
"cdna_end": null,
"cdna_length": 945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.248C>T",
"hgvs_p": "p.Ser83Leu",
"transcript": "XM_047428770.1",
"protein_id": "XP_047284726.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 159,
"cds_start": 248,
"cds_end": null,
"cds_length": 480,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 4156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Ser82Leu",
"transcript": "XM_011538269.3",
"protein_id": "XP_011536571.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 158,
"cds_start": 245,
"cds_end": null,
"cds_length": 477,
"cdna_start": 840,
"cdna_end": null,
"cdna_length": 4385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "c.366C>T",
"hgvs_p": "p.Val122Val",
"transcript": "XM_011538267.4",
"protein_id": "XP_011536569.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 165,
"cds_start": 366,
"cds_end": null,
"cds_length": 498,
"cdna_start": 711,
"cdna_end": null,
"cdna_length": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*86C>T",
"hgvs_p": null,
"transcript": "ENST00000537496.5",
"protein_id": "ENSP00000444793.1",
"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": 1188,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*224C>T",
"hgvs_p": null,
"transcript": "ENST00000541763.6",
"protein_id": "ENSP00000474981.1",
"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": 1252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*402C>T",
"hgvs_p": null,
"transcript": "ENST00000544051.5",
"protein_id": "ENSP00000438079.1",
"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": 1089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.632C>T",
"hgvs_p": null,
"transcript": "NR_038118.2",
"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": 4177,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*86C>T",
"hgvs_p": null,
"transcript": "ENST00000537496.5",
"protein_id": "ENSP00000444793.1",
"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": 1188,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*224C>T",
"hgvs_p": null,
"transcript": "ENST00000541763.6",
"protein_id": "ENSP00000474981.1",
"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": 1252,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"hgvs_c": "n.*402C>T",
"hgvs_p": null,
"transcript": "ENST00000544051.5",
"protein_id": "ENSP00000438079.1",
"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": 1089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MMAB",
"gene_hgnc_id": 19331,
"dbsnp": "rs140881518",
"frequency_reference_population": 0.000032926986,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000294985,
"gnomad_genomes_af": 0.0000658241,
"gnomad_exomes_ac": 43,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9610917568206787,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8420000076293945,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.943,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4953,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.152,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.964988688415973,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,PP5",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000545712.7",
"gene_symbol": "MMAB",
"hgnc_id": 19331,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.521C>T",
"hgvs_p": "p.Ser174Leu"
}
],
"clinvar_disease": " cblB type,MMAB-related disorder,Methylmalonic aciduria,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:3 US:1",
"phenotype_combined": "not provided|Methylmalonic aciduria, cblB type|MMAB-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}