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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: 4-13381577-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=13381577&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 13381577,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000330852.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "NM_001017979.3",
"protein_id": "NP_001017979.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 221,
"cds_start": 409,
"cds_end": null,
"cds_length": 666,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1690,
"mane_select": "ENST00000330852.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "ENST00000330852.10",
"protein_id": "ENSP00000328551.5",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 221,
"cds_start": 409,
"cds_end": null,
"cds_length": 666,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1690,
"mane_select": "NM_001017979.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "NM_004249.4",
"protein_id": "NP_004240.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 220,
"cds_start": 409,
"cds_end": null,
"cds_length": 663,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1785,
"mane_select": null,
"mane_plus": "ENST00000288723.9",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "ENST00000288723.9",
"protein_id": "ENSP00000288723.4",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 220,
"cds_start": 409,
"cds_end": null,
"cds_length": 663,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1785,
"mane_select": null,
"mane_plus": "NM_004249.4",
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "n.279C>T",
"hgvs_p": null,
"transcript": "ENST00000508274.5",
"protein_id": "ENSP00000424043.1",
"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": 1551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "NM_001159601.2",
"protein_id": "NP_001153073.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 204,
"cds_start": 409,
"cds_end": null,
"cds_length": 615,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*",
"transcript": "ENST00000338176.8",
"protein_id": "ENSP00000340079.4",
"transcript_support_level": 3,
"aa_start": 137,
"aa_end": null,
"aa_length": 204,
"cds_start": 409,
"cds_end": null,
"cds_length": 615,
"cdna_start": 624,
"cdna_end": null,
"cdna_length": 1787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59*",
"transcript": "ENST00000511649.5",
"protein_id": "ENSP00000424899.1",
"transcript_support_level": 5,
"aa_start": 59,
"aa_end": null,
"aa_length": 142,
"cds_start": 175,
"cds_end": null,
"cds_length": 429,
"cdna_start": 176,
"cdna_end": null,
"cdna_length": 715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6*",
"transcript": "ENST00000504644.1",
"protein_id": "ENSP00000422816.1",
"transcript_support_level": 5,
"aa_start": 6,
"aa_end": null,
"aa_length": 73,
"cds_start": 16,
"cds_end": null,
"cds_length": 222,
"cdna_start": 18,
"cdna_end": null,
"cdna_length": 405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"hgvs_c": "c.279C>T",
"hgvs_p": "p.Cys93Cys",
"transcript": "ENST00000630951.1",
"protein_id": "ENSP00000485808.1",
"transcript_support_level": 5,
"aa_start": 93,
"aa_end": null,
"aa_length": 95,
"cds_start": 279,
"cds_end": null,
"cds_length": 288,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAB28",
"gene_hgnc_id": 9768,
"dbsnp": "rs398123044",
"frequency_reference_population": 0.000005582912,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.0000047943,
"gnomad_genomes_af": 0.0000131582,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1979999989271164,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.198,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.258,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000330852.10",
"gene_symbol": "RAB28",
"hgnc_id": 9768,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137*"
}
],
"clinvar_disease": "Cone-rod dystrophy,Cone-rod dystrophy 18",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Cone-rod dystrophy 18|Cone-rod dystrophy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}