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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: 3-38138692-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38138692&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38138692,
"ref": "C",
"alt": "G",
"effect": "5_prime_UTR_variant",
"transcript": "ENST00000650905.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.42C>G",
"hgvs_p": null,
"transcript": "ENST00000416282.3",
"protein_id": null,
"transcript_support_level": 1,
"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": 2725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "NM_002468.5",
"protein_id": "NP_002459.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 296,
"cds_start": -4,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": "ENST00000650905.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "ENST00000650905.2",
"protein_id": "ENSP00000498360.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 296,
"cds_start": -4,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": "NM_002468.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "ENST00000421516.3",
"protein_id": "ENSP00000391753.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 304,
"cds_start": -4,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "ENST00000417037.8",
"protein_id": "ENSP00000401399.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": -4,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2638,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.36C>G",
"hgvs_p": null,
"transcript": "ENST00000460295.1",
"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": 1088,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.58C>G",
"hgvs_p": null,
"transcript": "ENST00000484513.2",
"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": 4102,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.32C>G",
"hgvs_p": null,
"transcript": "ENST00000652590.1",
"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": 2839,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.58C>G",
"hgvs_p": null,
"transcript": "ENST00000699084.1",
"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": 3706,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "n.22C>G",
"hgvs_p": null,
"transcript": "ENST00000699085.1",
"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": 3482,
"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": "ENSG00000299092",
"gene_hgnc_id": null,
"hgvs_c": "n.586G>C",
"hgvs_p": null,
"transcript": "ENST00000760417.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 1521,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "NM_001172567.2",
"protein_id": "NP_001166038.2",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
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"transcript": "NM_001172568.2",
"protein_id": "NP_001166039.2",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 251,
"cds_start": -4,
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},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": 1,
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"exon_count": 5,
"intron_rank": null,
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"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "NM_001365876.1",
"protein_id": "NP_001352805.1",
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"cds_start": -4,
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},
{
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"protein_coding": true,
"strand": true,
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"5_prime_UTR_variant"
],
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"exon_count": 5,
"intron_rank": null,
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"gene_symbol": "MYD88",
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"hgvs_c": "c.-9C>G",
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"transcript": "ENST00000652213.1",
"protein_id": "ENSP00000498576.1",
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
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"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "NM_001374787.1",
"protein_id": "NP_001361716.1",
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},
{
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"5_prime_UTR_variant"
],
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"gene_symbol": "MYD88",
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"hgvs_c": "c.-9C>G",
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"transcript": "NM_001365877.1",
"protein_id": "NP_001352806.1",
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "NM_001172569.3",
"protein_id": "NP_001166040.2",
"transcript_support_level": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
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"hgvs_c": "c.-9C>G",
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"transcript": "ENST00000651800.2",
"protein_id": "ENSP00000499012.2",
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},
{
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"strand": true,
"consequences": [
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],
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"gene_symbol": "MYD88",
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"transcript": "NM_001172566.2",
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-9C>G",
"hgvs_p": null,
"transcript": "ENST00000650112.2",
"protein_id": "ENSP00000497991.2",
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"hgvs_c": "c.-75C>G",
"hgvs_p": null,
"transcript": "ENST00000699086.1",
"protein_id": "ENSP00000514121.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": -4,
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"cds_length": 537,
"cdna_start": null,
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"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYD88",
"gene_hgnc_id": 7562,
"dbsnp": "rs587778544",
"frequency_reference_population": 0.000042593118,
"hom_count_reference_population": 0,
"allele_count_reference_population": 68,
"gnomad_exomes_af": 0.0000408546,
"gnomad_genomes_af": 0.0000590722,
"gnomad_exomes_ac": 59,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.052211642265319824,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.014,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.347,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000650905.2",
"gene_symbol": "MYD88",
"hgnc_id": 7562,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-9C>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000760417.1",
"gene_symbol": "ENSG00000299092",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.586G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Pyogenic bacterial infections due to MyD88 deficiency,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3 O:1",
"phenotype_combined": "not specified|Pyogenic bacterial infections due to MyD88 deficiency|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}