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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: 1-212895246-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=212895246&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FLVCR1",
"hgnc_id": 24682,
"hgvs_c": "c.1624C>T",
"hgvs_p": "p.Pro542Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -16,
"transcript": "NM_014053.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_score": -16,
"allele_count_reference_population": 283,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0677,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "FLVCR1-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.004611074924468994,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 555,
"aa_ref": "P",
"aa_start": 542,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5919,
"cdna_start": 1802,
"cds_end": null,
"cds_length": 1668,
"cds_start": 1624,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_014053.4",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1624C>T",
"hgvs_p": "p.Pro542Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366971.9",
"protein_coding": true,
"protein_id": "NP_054772.1",
"strand": true,
"transcript": "NM_014053.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 555,
"aa_ref": "P",
"aa_start": 542,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5919,
"cdna_start": 1802,
"cds_end": null,
"cds_length": 1668,
"cds_start": 1624,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000366971.9",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1624C>T",
"hgvs_p": "p.Pro542Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014053.4",
"protein_coding": true,
"protein_id": "ENSP00000355938.4",
"strand": true,
"transcript": "ENST00000366971.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 585,
"aa_ref": "P",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3534,
"cdna_start": 1891,
"cds_end": null,
"cds_length": 1758,
"cds_start": 1714,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000867613.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Pro572Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537672.1",
"strand": true,
"transcript": "ENST00000867613.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 564,
"aa_ref": "P",
"aa_start": 551,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2332,
"cdna_start": 1862,
"cds_end": null,
"cds_length": 1695,
"cds_start": 1651,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000971333.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1651C>T",
"hgvs_p": "p.Pro551Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641392.1",
"strand": true,
"transcript": "ENST00000971333.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 531,
"aa_ref": "P",
"aa_start": 518,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3410,
"cdna_start": 1768,
"cds_end": null,
"cds_length": 1596,
"cds_start": 1552,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930967.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1552C>T",
"hgvs_p": "p.Pro518Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601026.1",
"strand": true,
"transcript": "ENST00000930967.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 353,
"aa_ref": "P",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1108,
"cdna_start": 1020,
"cds_end": null,
"cds_length": 1062,
"cds_start": 1018,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000419102.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.1018C>T",
"hgvs_p": "p.Pro340Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414680.1",
"strand": true,
"transcript": "ENST00000419102.1",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 330,
"aa_ref": "P",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1259,
"cdna_start": 1092,
"cds_end": null,
"cds_length": 993,
"cds_start": 949,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000930968.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Pro317Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601027.1",
"strand": true,
"transcript": "ENST00000930968.1",
"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": 599,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000483790.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "n.451C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483790.1",
"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": 5551,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XR_007059232.1",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "n.1691C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007059232.1",
"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": 5662,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XR_247024.4",
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"hgvs_c": "n.1802C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_247024.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs141575859",
"effect": "missense_variant",
"frequency_reference_population": 0.00017541033,
"gene_hgnc_id": 24682,
"gene_symbol": "FLVCR1",
"gnomad_exomes_ac": 119,
"gnomad_exomes_af": 0.0000814334,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 164,
"gnomad_genomes_af": 0.00107864,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|not specified|FLVCR1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.016,
"pos": 212895246,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.251,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014053.4"
}
]
}