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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: 4-39288823-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39288823&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 39288823,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001204747.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3382C>T",
"hgvs_p": "p.Pro1128Ser",
"transcript": "NM_002913.5",
"protein_id": "NP_002904.3",
"transcript_support_level": null,
"aa_start": 1128,
"aa_end": null,
"aa_length": 1147,
"cds_start": 3382,
"cds_end": null,
"cds_length": 3444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000349703.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002913.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3382C>T",
"hgvs_p": "p.Pro1128Ser",
"transcript": "ENST00000349703.7",
"protein_id": "ENSP00000261424.4",
"transcript_support_level": 1,
"aa_start": 1128,
"aa_end": null,
"aa_length": 1147,
"cds_start": 3382,
"cds_end": null,
"cds_length": 3444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002913.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000349703.7"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3385C>T",
"hgvs_p": "p.Pro1129Ser",
"transcript": "ENST00000381897.5",
"protein_id": "ENSP00000371321.1",
"transcript_support_level": 1,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3385,
"cds_end": null,
"cds_length": 3447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381897.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3430C>T",
"hgvs_p": "p.Pro1144Ser",
"transcript": "ENST00000906184.1",
"protein_id": "ENSP00000576243.1",
"transcript_support_level": null,
"aa_start": 1144,
"aa_end": null,
"aa_length": 1163,
"cds_start": 3430,
"cds_end": null,
"cds_length": 3492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906184.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3418C>T",
"hgvs_p": "p.Pro1140Ser",
"transcript": "ENST00000967837.1",
"protein_id": "ENSP00000637896.1",
"transcript_support_level": null,
"aa_start": 1140,
"aa_end": null,
"aa_length": 1159,
"cds_start": 3418,
"cds_end": null,
"cds_length": 3480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967837.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3385C>T",
"hgvs_p": "p.Pro1129Ser",
"transcript": "NM_001204747.2",
"protein_id": "NP_001191676.1",
"transcript_support_level": null,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3385,
"cds_end": null,
"cds_length": 3447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204747.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3331C>T",
"hgvs_p": "p.Pro1111Ser",
"transcript": "ENST00000923045.1",
"protein_id": "ENSP00000593103.1",
"transcript_support_level": null,
"aa_start": 1111,
"aa_end": null,
"aa_length": 1130,
"cds_start": 3331,
"cds_end": null,
"cds_length": 3393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923045.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3307C>T",
"hgvs_p": "p.Pro1103Ser",
"transcript": "NM_001363496.2",
"protein_id": "NP_001350425.1",
"transcript_support_level": null,
"aa_start": 1103,
"aa_end": null,
"aa_length": 1122,
"cds_start": 3307,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363496.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3307C>T",
"hgvs_p": "p.Pro1103Ser",
"transcript": "ENST00000906185.1",
"protein_id": "ENSP00000576244.1",
"transcript_support_level": null,
"aa_start": 1103,
"aa_end": null,
"aa_length": 1122,
"cds_start": 3307,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906185.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3307C>T",
"hgvs_p": "p.Pro1103Ser",
"transcript": "ENST00000923043.1",
"protein_id": "ENSP00000593102.1",
"transcript_support_level": null,
"aa_start": 1103,
"aa_end": null,
"aa_length": 1122,
"cds_start": 3307,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923043.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3304C>T",
"hgvs_p": "p.Pro1102Ser",
"transcript": "NM_001363495.2",
"protein_id": "NP_001350424.1",
"transcript_support_level": null,
"aa_start": 1102,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3304,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363495.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3304C>T",
"hgvs_p": "p.Pro1102Ser",
"transcript": "ENST00000906183.1",
"protein_id": "ENSP00000576242.1",
"transcript_support_level": null,
"aa_start": 1102,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3304,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906183.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3304C>T",
"hgvs_p": "p.Pro1102Ser",
"transcript": "ENST00000906186.1",
"protein_id": "ENSP00000576245.1",
"transcript_support_level": null,
"aa_start": 1102,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3304,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906186.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.3229C>T",
"hgvs_p": "p.Pro1077Ser",
"transcript": "ENST00000923042.1",
"protein_id": "ENSP00000593101.1",
"transcript_support_level": null,
"aa_start": 1077,
"aa_end": null,
"aa_length": 1096,
"cds_start": 3229,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923042.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2932C>T",
"hgvs_p": "p.Pro978Ser",
"transcript": "ENST00000967836.1",
"protein_id": "ENSP00000637895.1",
"transcript_support_level": null,
"aa_start": 978,
"aa_end": null,
"aa_length": 997,
"cds_start": 2932,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967836.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2590C>T",
"hgvs_p": "p.Pro864Ser",
"transcript": "ENST00000923046.1",
"protein_id": "ENSP00000593105.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 883,
"cds_start": 2590,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923046.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2875C>T",
"hgvs_p": "p.Pro959Ser",
"transcript": "XM_011513731.2",
"protein_id": "XP_011512033.1",
"transcript_support_level": null,
"aa_start": 959,
"aa_end": null,
"aa_length": 978,
"cds_start": 2875,
"cds_end": null,
"cds_length": 2937,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513731.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2797C>T",
"hgvs_p": "p.Pro933Ser",
"transcript": "XM_047416054.1",
"protein_id": "XP_047272010.1",
"transcript_support_level": null,
"aa_start": 933,
"aa_end": null,
"aa_length": 952,
"cds_start": 2797,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416054.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "n.523C>T",
"hgvs_p": null,
"transcript": "ENST00000502991.5",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000502991.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "n.487C>T",
"hgvs_p": null,
"transcript": "ENST00000504974.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000504974.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "n.597C>T",
"hgvs_p": null,
"transcript": "ENST00000510783.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000510783.5"
}
],
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"dbsnp": "rs755561864",
"frequency_reference_population": 0.000015526697,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000157646,
"gnomad_genomes_af": 0.0000132308,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014418721199035645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.071,
"revel_prediction": "Benign",
"alphamissense_score": 0.0662,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.342,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001204747.2",
"gene_symbol": "RFC1",
"hgnc_id": 9969,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3385C>T",
"hgvs_p": "p.Pro1129Ser"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}