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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: 3-53105743-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=53105743&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RFT1",
"hgnc_id": 30220,
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_052859.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate",
"acmg_score": 6,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.2545,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.4,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9267561435699463,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 541,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5081,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1626,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_052859.4",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296292.8",
"protein_coding": true,
"protein_id": "NP_443091.1",
"strand": false,
"transcript": "NM_052859.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 541,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5081,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1626,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000296292.8",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_052859.4",
"protein_coding": true,
"protein_id": "ENSP00000296292.3",
"strand": false,
"transcript": "ENST00000296292.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 603,
"aa_ref": "I",
"aa_start": 358,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2099,
"cdna_start": 1108,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1073,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000909797.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.1073T>C",
"hgvs_p": "p.Ile358Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579856.1",
"strand": false,
"transcript": "ENST00000909797.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 567,
"aa_ref": "I",
"aa_start": 322,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1992,
"cdna_start": 1000,
"cds_end": null,
"cds_length": 1704,
"cds_start": 965,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000968203.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.965T>C",
"hgvs_p": "p.Ile322Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638262.1",
"strand": false,
"transcript": "ENST00000968203.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 540,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1957,
"cdna_start": 941,
"cds_end": null,
"cds_length": 1623,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000909796.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579855.1",
"strand": false,
"transcript": "ENST00000909796.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 524,
"aa_ref": "I",
"aa_start": 279,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2030,
"cdna_start": 892,
"cds_end": null,
"cds_length": 1575,
"cds_start": 836,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000909795.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.836T>C",
"hgvs_p": "p.Ile279Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579854.1",
"strand": false,
"transcript": "ENST00000909795.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 507,
"aa_ref": "I",
"aa_start": 262,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1831,
"cdna_start": 839,
"cds_end": null,
"cds_length": 1524,
"cds_start": 785,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000968202.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.785T>C",
"hgvs_p": "p.Ile262Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638261.1",
"strand": false,
"transcript": "ENST00000968202.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 502,
"aa_ref": "I",
"aa_start": 257,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1800,
"cdna_start": 823,
"cds_end": null,
"cds_length": 1509,
"cds_start": 770,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000394738.7",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378223.3",
"strand": false,
"transcript": "ENST00000394738.7",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 465,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3963,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1398,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000850556.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520849.1",
"strand": false,
"transcript": "ENST00000850556.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 330,
"aa_ref": "I",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4475,
"cdna_start": 326,
"cds_end": null,
"cds_length": 993,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000909794.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Ile85Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579853.1",
"strand": false,
"transcript": "ENST00000909794.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 290,
"aa_ref": "I",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 886,
"cdna_start": 760,
"cds_end": null,
"cds_length": 875,
"cds_start": 749,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000467048.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.749T>C",
"hgvs_p": "p.Ile250Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420325.1",
"strand": false,
"transcript": "ENST00000467048.1",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 477,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9901,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1434,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011534214.3",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532516.1",
"strand": false,
"transcript": "XM_011534214.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 464,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7680,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1395,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011534215.4",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532517.1",
"strand": false,
"transcript": "XM_011534215.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 403,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3157,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1212,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_006713384.4",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713447.1",
"strand": false,
"transcript": "XM_006713384.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 384,
"aa_ref": "I",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1209,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1155,
"cds_start": 887,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_005265537.5",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Ile296Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265594.1",
"strand": false,
"transcript": "XM_005265537.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 322,
"aa_ref": "I",
"aa_start": 77,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4436,
"cdna_start": 277,
"cds_end": null,
"cds_length": 969,
"cds_start": 230,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011534216.4",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "c.230T>C",
"hgvs_p": "p.Ile77Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532518.1",
"strand": false,
"transcript": "XM_011534216.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 924,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000471158.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "n.329T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000471158.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7870,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XR_007095765.1",
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"hgvs_c": "n.922T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007095765.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs772820136",
"effect": "missense_variant",
"frequency_reference_population": 0.000004105321,
"gene_hgnc_id": 30220,
"gene_symbol": "RFT1",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000410532,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Inborn genetic diseases",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.863,
"pos": 53105743,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.92,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_052859.4"
}
]
}