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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: 6-129492363-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=129492363&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 129492363,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000426.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.8124T>A",
"hgvs_p": "p.Gly2708Gly",
"transcript": "NM_000426.4",
"protein_id": "NP_000417.3",
"transcript_support_level": null,
"aa_start": 2708,
"aa_end": null,
"aa_length": 3122,
"cds_start": 8124,
"cds_end": null,
"cds_length": 9369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000421865.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000426.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.8124T>A",
"hgvs_p": "p.Gly2708Gly",
"transcript": "ENST00000421865.3",
"protein_id": "ENSP00000400365.2",
"transcript_support_level": 5,
"aa_start": 2708,
"aa_end": null,
"aa_length": 3122,
"cds_start": 8124,
"cds_end": null,
"cds_length": 9369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000426.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421865.3"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.8388T>A",
"hgvs_p": "p.Gly2796Gly",
"transcript": "ENST00000618192.5",
"protein_id": "ENSP00000480802.2",
"transcript_support_level": 5,
"aa_start": 2796,
"aa_end": null,
"aa_length": 3210,
"cds_start": 8388,
"cds_end": null,
"cds_length": 9633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618192.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.8112T>A",
"hgvs_p": "p.Gly2704Gly",
"transcript": "NM_001079823.2",
"protein_id": "NP_001073291.2",
"transcript_support_level": null,
"aa_start": 2704,
"aa_end": null,
"aa_length": 3118,
"cds_start": 8112,
"cds_end": null,
"cds_length": 9357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001079823.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.8112T>A",
"hgvs_p": "p.Gly2704Gly",
"transcript": "ENST00000617695.5",
"protein_id": "ENSP00000481744.2",
"transcript_support_level": 5,
"aa_start": 2704,
"aa_end": null,
"aa_length": 3118,
"cds_start": 8112,
"cds_end": null,
"cds_length": 9357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000617695.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.189T>A",
"hgvs_p": "p.Gly63Gly",
"transcript": "ENST00000494137.2",
"protein_id": "ENSP00000510626.1",
"transcript_support_level": 3,
"aa_start": 63,
"aa_end": null,
"aa_length": 477,
"cds_start": 189,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494137.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.189T>A",
"hgvs_p": "p.Gly63Gly",
"transcript": "ENST00000498257.6",
"protein_id": "ENSP00000510533.1",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 477,
"cds_start": 189,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000498257.6"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.189T>A",
"hgvs_p": "p.Gly63Gly",
"transcript": "ENST00000688799.1",
"protein_id": "ENSP00000508458.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 477,
"cds_start": 189,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688799.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226149",
"gene_hgnc_id": null,
"hgvs_c": "n.2923A>T",
"hgvs_p": null,
"transcript": "ENST00000657779.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000657779.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "n.1102T>A",
"hgvs_p": null,
"transcript": "ENST00000688198.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000688198.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "n.1118T>A",
"hgvs_p": null,
"transcript": "ENST00000690858.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000690858.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226149",
"gene_hgnc_id": null,
"hgvs_c": "n.1372+8099A>T",
"hgvs_p": null,
"transcript": "ENST00000664071.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000664071.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226149",
"gene_hgnc_id": null,
"hgvs_c": "n.975+10242A>T",
"hgvs_p": null,
"transcript": "ENST00000665046.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000665046.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC102723409",
"gene_hgnc_id": null,
"hgvs_c": "n.*119A>T",
"hgvs_p": null,
"transcript": "XR_001743860.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001743860.2"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC102723409",
"gene_hgnc_id": null,
"hgvs_c": "n.*119A>T",
"hgvs_p": null,
"transcript": "XR_007059756.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007059756.1"
}
],
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"dbsnp": "rs34997144",
"frequency_reference_population": 0.0031793627,
"hom_count_reference_population": 101,
"allele_count_reference_population": 5132,
"gnomad_exomes_af": 0.00185659,
"gnomad_genomes_af": 0.0158724,
"gnomad_exomes_ac": 2714,
"gnomad_genomes_ac": 2418,
"gnomad_exomes_homalt": 57,
"gnomad_genomes_homalt": 44,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5099999904632568,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.184,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000426.4",
"gene_symbol": "LAMA2",
"hgnc_id": 6482,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8124T>A",
"hgvs_p": "p.Gly2708Gly"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000657779.1",
"gene_symbol": "ENSG00000226149",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2923A>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_001743860.2",
"gene_symbol": "LOC102723409",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*119A>T",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital muscular dystrophy due to partial LAMA2 deficiency,LAMA2-related muscular dystrophy,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Congenital muscular dystrophy due to partial LAMA2 deficiency|LAMA2-related muscular dystrophy|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}