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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: 4-113903100-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=113903100&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"PP3",
"BP4_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ARSJ",
"hgnc_id": 26286,
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"inheritance_mode": "AR",
"pathogenic_score": 1,
"score": -7,
"transcript": "NM_024590.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BS2",
"acmg_score": -7,
"allele_count_reference_population": 445,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9805,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.55,
"chr": "4",
"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": 0.05702880024909973,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 599,
"aa_ref": "S",
"aa_start": 325,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4603,
"cdna_start": 1787,
"cds_end": null,
"cds_length": 1800,
"cds_start": 974,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_024590.4",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000315366.8",
"protein_coding": true,
"protein_id": "NP_078866.3",
"strand": false,
"transcript": "NM_024590.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 599,
"aa_ref": "S",
"aa_start": 325,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4603,
"cdna_start": 1787,
"cds_end": null,
"cds_length": 1800,
"cds_start": 974,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000315366.8",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024590.4",
"protein_coding": true,
"protein_id": "ENSP00000320219.7",
"strand": false,
"transcript": "ENST00000315366.8",
"transcript_support_level": 1
},
{
"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": 2253,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000509829.1",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "n.*653C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421327.1",
"strand": false,
"transcript": "ENST00000509829.1",
"transcript_support_level": 1
},
{
"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": 2253,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000509829.1",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "n.*653C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421327.1",
"strand": false,
"transcript": "ENST00000509829.1",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 596,
"aa_ref": "S",
"aa_start": 325,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4507,
"cdna_start": 1787,
"cds_end": null,
"cds_length": 1791,
"cds_start": 974,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001354210.2",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341139.1",
"strand": false,
"transcript": "NM_001354210.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 480,
"aa_ref": "S",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4804,
"cdna_start": 2084,
"cds_end": null,
"cds_length": 1443,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001354211.2",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Ser209Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341140.1",
"strand": false,
"transcript": "NM_001354211.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 599,
"aa_ref": "S",
"aa_start": 325,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4240,
"cdna_start": 1424,
"cds_end": null,
"cds_length": 1800,
"cds_start": 974,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017008592.3",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864081.1",
"strand": false,
"transcript": "XM_017008592.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 596,
"aa_ref": "S",
"aa_start": 325,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4144,
"cdna_start": 1424,
"cds_end": null,
"cds_length": 1791,
"cds_start": 974,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047416154.1",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Ser325Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272110.1",
"strand": false,
"transcript": "XM_047416154.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 492,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4014,
"cdna_start": 1198,
"cds_end": null,
"cds_length": 1479,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011532238.4",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.653C>T",
"hgvs_p": "p.Ser218Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530540.1",
"strand": false,
"transcript": "XM_011532238.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 489,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3918,
"cdna_start": 1198,
"cds_end": null,
"cds_length": 1470,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_024454215.2",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.653C>T",
"hgvs_p": "p.Ser218Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309983.1",
"strand": false,
"transcript": "XM_024454215.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 483,
"aa_ref": "S",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4807,
"cdna_start": 1991,
"cds_end": null,
"cds_length": 1452,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017008594.3",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Ser209Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864083.1",
"strand": false,
"transcript": "XM_017008594.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 483,
"aa_ref": "S",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3881,
"cdna_start": 1065,
"cds_end": null,
"cds_length": 1452,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047416155.1",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Ser209Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272111.1",
"strand": false,
"transcript": "XM_047416155.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 480,
"aa_ref": "S",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3785,
"cdna_start": 1065,
"cds_end": null,
"cds_length": 1443,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047416157.1",
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Ser209Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272113.1",
"strand": false,
"transcript": "XM_047416157.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201123448",
"effect": "missense_variant",
"frequency_reference_population": 0.00027570056,
"gene_hgnc_id": 26286,
"gene_symbol": "ARSJ",
"gnomad_exomes_ac": 397,
"gnomad_exomes_af": 0.000271568,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 48,
"gnomad_genomes_af": 0.000315395,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.789,
"pos": 113903100,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.842,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_024590.4"
}
]
}