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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: 16-29457656-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=29457656&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLX1B",
"hgnc_id": 28748,
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Pro203Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_024044.5",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SLX1B-SULT1A4",
"hgnc_id": 48353,
"hgvs_c": "n.550C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000344620.10",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": null,
"alphamissense_prediction": null,
"alphamissense_score": 0.184,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "16",
"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": 0.12426537275314331,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 275,
"aa_ref": "P",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1133,
"cdna_start": 817,
"cds_end": null,
"cds_length": 828,
"cds_start": 607,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_024044.5",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Pro203Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000330181.10",
"protein_coding": true,
"protein_id": "NP_076949.1",
"strand": true,
"transcript": "NM_024044.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 275,
"aa_ref": "P",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1133,
"cdna_start": 817,
"cds_end": null,
"cds_length": 828,
"cds_start": 607,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000330181.10",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Pro203Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024044.5",
"protein_coding": true,
"protein_id": "ENSP00000328940.5",
"strand": true,
"transcript": "ENST00000330181.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 161,
"aa_ref": "P",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 762,
"cdna_start": 446,
"cds_end": null,
"cds_length": 486,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000351581.4",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.265C>T",
"hgvs_p": "p.Pro89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000335316.4",
"strand": true,
"transcript": "ENST00000351581.4",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 273,
"aa_ref": "P",
"aa_start": 201,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1128,
"cdna_start": 811,
"cds_end": null,
"cds_length": 822,
"cds_start": 601,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001400286.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.601C>T",
"hgvs_p": "p.Pro201Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001387215.1",
"strand": true,
"transcript": "NM_001400286.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 237,
"aa_ref": "P",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1019,
"cdna_start": 703,
"cds_end": null,
"cds_length": 714,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000856228.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.493C>T",
"hgvs_p": "p.Pro165Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526287.1",
"strand": true,
"transcript": "ENST00000856228.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 161,
"aa_ref": "P",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 791,
"cdna_start": 475,
"cds_end": null,
"cds_length": 486,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_178044.4",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.265C>T",
"hgvs_p": "p.Pro89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_835145.1",
"strand": true,
"transcript": "NM_178044.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 123,
"aa_ref": "P",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 681,
"cdna_start": 361,
"cds_end": null,
"cds_length": 372,
"cds_start": 151,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000925429.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.151C>T",
"hgvs_p": "p.Pro51Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595488.1",
"strand": true,
"transcript": "ENST00000925429.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 101,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 611,
"cdna_start": null,
"cds_end": null,
"cds_length": 306,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001400287.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "c.189-272C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001387216.1",
"strand": true,
"transcript": "NM_001400287.1",
"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": 2424,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000344620.10",
"gene_hgnc_id": 48353,
"gene_symbol": "SLX1B-SULT1A4",
"hgvs_c": "n.550C>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": "ENST00000344620.10",
"transcript_support_level": 2
},
{
"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": 2380,
"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": "ENST00000395400.4",
"gene_hgnc_id": 48353,
"gene_symbol": "SLX1B-SULT1A4",
"hgvs_c": "n.1209C>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": "ENST00000395400.4",
"transcript_support_level": 2
},
{
"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": 2225,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000564950.5",
"gene_hgnc_id": 48353,
"gene_symbol": "SLX1B-SULT1A4",
"hgvs_c": "n.754C>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": "ENST00000564950.5",
"transcript_support_level": 2
},
{
"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": 1558,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000565219.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "n.1272C>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": "ENST00000565219.1",
"transcript_support_level": 2
},
{
"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": 1140,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000566424.1",
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"hgvs_c": "n.687C>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": "ENST00000566424.1",
"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": 2214,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_037609.1",
"gene_hgnc_id": 48353,
"gene_symbol": "SLX1B-SULT1A4",
"hgvs_c": "n.726C>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": "NR_037609.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1371942771",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 28748,
"gene_symbol": "SLX1B",
"gnomad_exomes_ac": 22,
"gnomad_exomes_af": 0.0000232264,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 13,
"gnomad_genomes_af": 0.000131144,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": null,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.356,
"pos": 29457656,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.028,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024044.5"
}
]
}