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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: 6-129481294-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=129481294&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 129481294,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000421865.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.7604G>A",
"hgvs_p": "p.Gly2535Asp",
"transcript": "NM_000426.4",
"protein_id": "NP_000417.3",
"transcript_support_level": null,
"aa_start": 2535,
"aa_end": null,
"aa_length": 3122,
"cds_start": 7604,
"cds_end": null,
"cds_length": 9369,
"cdna_start": 7712,
"cdna_end": null,
"cdna_length": 9696,
"mane_select": "ENST00000421865.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.7604G>A",
"hgvs_p": "p.Gly2535Asp",
"transcript": "ENST00000421865.3",
"protein_id": "ENSP00000400365.2",
"transcript_support_level": 5,
"aa_start": 2535,
"aa_end": null,
"aa_length": 3122,
"cds_start": 7604,
"cds_end": null,
"cds_length": 9369,
"cdna_start": 7712,
"cdna_end": null,
"cdna_length": 9696,
"mane_select": "NM_000426.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.7868G>A",
"hgvs_p": "p.Gly2623Asp",
"transcript": "ENST00000618192.5",
"protein_id": "ENSP00000480802.2",
"transcript_support_level": 5,
"aa_start": 2623,
"aa_end": null,
"aa_length": 3210,
"cds_start": 7868,
"cds_end": null,
"cds_length": 9633,
"cdna_start": 7976,
"cdna_end": null,
"cdna_length": 9960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.7592G>A",
"hgvs_p": "p.Gly2531Asp",
"transcript": "NM_001079823.2",
"protein_id": "NP_001073291.2",
"transcript_support_level": null,
"aa_start": 2531,
"aa_end": null,
"aa_length": 3118,
"cds_start": 7592,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 7700,
"cdna_end": null,
"cdna_length": 9684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"hgvs_c": "c.7592G>A",
"hgvs_p": "p.Gly2531Asp",
"transcript": "ENST00000617695.5",
"protein_id": "ENSP00000481744.2",
"transcript_support_level": 5,
"aa_start": 2531,
"aa_end": null,
"aa_length": 3118,
"cds_start": 7592,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 7700,
"cdna_end": null,
"cdna_length": 9656,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000233351",
"gene_hgnc_id": null,
"hgvs_c": "n.117C>T",
"hgvs_p": null,
"transcript": "ENST00000442449.1",
"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": 391,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901401",
"gene_hgnc_id": null,
"hgvs_c": "n.5089C>T",
"hgvs_p": null,
"transcript": "XR_007059767.1",
"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": 6770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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+21311C>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAMA2",
"gene_hgnc_id": 6482,
"dbsnp": "rs374210667",
"frequency_reference_population": 0.00001611304,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000136834,
"gnomad_genomes_af": 0.0000394799,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9460694789886475,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.939,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9507,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.374,
"phylop100way_prediction": "Pathogenic",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Strong,BP6",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000421865.3",
"gene_symbol": "LAMA2",
"hgnc_id": 6482,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7604G>A",
"hgvs_p": "p.Gly2535Asp"
},
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007059767.1",
"gene_symbol": "LOC124901401",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.5089C>T",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000442449.1",
"gene_symbol": "ENSG00000233351",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.117C>T",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000665046.1",
"gene_symbol": "ENSG00000226149",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.975+21311C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,LAMA2-related muscular dystrophy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "LAMA2-related muscular dystrophy|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}