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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: 6-143428628-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=143428628&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 143428628,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_182503.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.516A>T",
"hgvs_p": "p.Lys172Asn",
"transcript": "NM_182503.3",
"protein_id": "NP_872309.2",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 191,
"cds_start": 516,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000237283.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182503.3"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.516A>T",
"hgvs_p": "p.Lys172Asn",
"transcript": "ENST00000237283.9",
"protein_id": "ENSP00000237283.8",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 191,
"cds_start": 516,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_182503.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237283.9"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.375A>T",
"hgvs_p": "p.Lys125Asn",
"transcript": "ENST00000606514.5",
"protein_id": "ENSP00000475651.1",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 144,
"cds_start": 375,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000606514.5"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Lys137Asn",
"transcript": "ENST00000933835.1",
"protein_id": "ENSP00000603894.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 156,
"cds_start": 411,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933835.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.375A>T",
"hgvs_p": "p.Lys125Asn",
"transcript": "NM_001286259.2",
"protein_id": "NP_001273188.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 144,
"cds_start": 375,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286259.2"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.153A>T",
"hgvs_p": "p.Lys51Asn",
"transcript": "ENST00000933836.1",
"protein_id": "ENSP00000603895.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 70,
"cds_start": 153,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933836.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Lys211Asn",
"transcript": "XM_011535439.3",
"protein_id": "XP_011533741.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 230,
"cds_start": 633,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011535439.3"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.375A>T",
"hgvs_p": "p.Lys125Asn",
"transcript": "XM_017010260.3",
"protein_id": "XP_016865749.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 144,
"cds_start": 375,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010260.3"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.375A>T",
"hgvs_p": "p.Lys125Asn",
"transcript": "XM_024446329.2",
"protein_id": "XP_024302097.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 144,
"cds_start": 375,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024446329.2"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.375A>T",
"hgvs_p": "p.Lys125Asn",
"transcript": "XM_047418189.1",
"protein_id": "XP_047274145.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 144,
"cds_start": 375,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418189.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"hgvs_c": "c.342A>T",
"hgvs_p": "p.Lys114Asn",
"transcript": "XM_017010263.2",
"protein_id": "XP_016865752.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 133,
"cds_start": 342,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010263.2"
}
],
"gene_symbol": "ADAT2",
"gene_hgnc_id": 21172,
"dbsnp": "rs754256938",
"frequency_reference_population": 0.000013631119,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.000013682,
"gnomad_genomes_af": 0.000013142,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.25293487310409546,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.117,
"revel_prediction": "Benign",
"alphamissense_score": 0.8761,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.506,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_182503.3",
"gene_symbol": "ADAT2",
"hgnc_id": 21172,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.516A>T",
"hgvs_p": "p.Lys172Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}