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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: 1-205569086-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=205569086&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC60A1",
"hgnc_id": 25433,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_181644.5",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MFSD4A",
"hgnc_id": 25433,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000367147.9",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SLC60A1-AS1",
"hgnc_id": 27632,
"hgvs_c": "n.177+43C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "NR_027086.2",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MFSD4A-AS1",
"hgnc_id": null,
"hgvs_c": "n.168+43C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000732930.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": 0.3172,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1041470468044281,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 514,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4058,
"cdna_start": 73,
"cds_end": null,
"cds_length": 1545,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_181644.5",
"gene_hgnc_id": 25433,
"gene_symbol": "SLC60A1",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000367147.9",
"protein_coding": true,
"protein_id": "NP_857595.3",
"strand": true,
"transcript": "NM_181644.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 514,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4058,
"cdna_start": 73,
"cds_end": null,
"cds_length": 1545,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000367147.9",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_181644.5",
"protein_coding": true,
"protein_id": "ENSP00000356115.4",
"strand": true,
"transcript": "ENST00000367147.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 513,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3701,
"cdna_start": 77,
"cds_end": null,
"cds_length": 1542,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000873628.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543687.1",
"strand": true,
"transcript": "ENST00000873628.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 505,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4055,
"cdna_start": 97,
"cds_end": null,
"cds_length": 1518,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000873627.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543686.1",
"strand": true,
"transcript": "ENST00000873627.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 456,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4064,
"cdna_start": 254,
"cds_end": null,
"cds_length": 1371,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000946000.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616059.1",
"strand": true,
"transcript": "ENST00000946000.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 427,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3831,
"cdna_start": 107,
"cds_end": null,
"cds_length": 1284,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000873626.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543685.1",
"strand": true,
"transcript": "ENST00000873626.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 418,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2488,
"cdna_start": 73,
"cds_end": null,
"cds_length": 1257,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000873629.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543688.1",
"strand": true,
"transcript": "ENST00000873629.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 361,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1136,
"cdna_start": 66,
"cds_end": null,
"cds_length": 1086,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000489709.5",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478732.1",
"strand": true,
"transcript": "ENST00000489709.5",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 332,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3154,
"cdna_start": 71,
"cds_end": null,
"cds_length": 999,
"cds_start": 17,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000946001.1",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Arg6His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616060.1",
"strand": true,
"transcript": "ENST00000946001.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1475,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000475956.5",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "n.17G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000482239.1",
"strand": true,
"transcript": "ENST00000475956.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1883,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000539267.5",
"gene_hgnc_id": 25433,
"gene_symbol": "MFSD4A",
"hgvs_c": "n.17G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000445329.1",
"strand": true,
"transcript": "ENST00000539267.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 525,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000732930.1",
"gene_hgnc_id": null,
"gene_symbol": "MFSD4A-AS1",
"hgvs_c": "n.168+43C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000732930.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 373,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000732931.1",
"gene_hgnc_id": null,
"gene_symbol": "MFSD4A-AS1",
"hgvs_c": "n.138+43C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000732931.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2985,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_027086.2",
"gene_hgnc_id": 27632,
"gene_symbol": "SLC60A1-AS1",
"hgvs_c": "n.177+43C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_027086.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3611,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_152721.1",
"gene_hgnc_id": 27632,
"gene_symbol": "SLC60A1-AS1",
"hgvs_c": "n.177+43C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_152721.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs747518493",
"effect": "missense_variant",
"frequency_reference_population": 0.000010041371,
"gene_hgnc_id": 25433,
"gene_symbol": "SLC60A1",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000446973,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.0000594232,
"gnomad_genomes_homalt": 0,
"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": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.501,
"pos": 205569086,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.103,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_181644.5"
}
]
}