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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: 3-57913179-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57913179&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLMAP",
"hgnc_id": 16643,
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Lys688Arg",
"inheritance_mode": "Unknown,AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_001377538.1",
"verdict": "Benign"
},
{
"benign_score": 5,
"criteria": [
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC105377103",
"hgnc_id": null,
"hgvs_c": "n.364+4005T>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -5,
"transcript": "XR_940867.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_score": -9,
"allele_count_reference_population": 605,
"alphamissense_prediction": null,
"alphamissense_score": 0.0749,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Brugada syndrome,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04608577489852905,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 842,
"aa_ref": "K",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6381,
"cdna_start": 3180,
"cds_end": null,
"cds_length": 2529,
"cds_start": 2042,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_001377540.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.2042A>G",
"hgvs_p": "p.Lys681Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000671191.1",
"protein_coding": true,
"protein_id": "NP_001364469.1",
"strand": true,
"transcript": "NM_001377540.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 842,
"aa_ref": "K",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6381,
"cdna_start": 3180,
"cds_end": null,
"cds_length": 2529,
"cds_start": 2042,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000671191.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.2042A>G",
"hgvs_p": "p.Lys681Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001377540.1",
"protein_coding": true,
"protein_id": "ENSP00000499458.1",
"strand": true,
"transcript": "ENST00000671191.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 804,
"aa_ref": "K",
"aa_start": 643,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5455,
"cdna_start": 3131,
"cds_end": null,
"cds_length": 2415,
"cds_start": 1928,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000417128.7",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1928A>G",
"hgvs_p": "p.Lys643Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000412829.3",
"strand": true,
"transcript": "ENST00000417128.7",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 790,
"aa_ref": "K",
"aa_start": 626,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4027,
"cdna_start": 1971,
"cds_end": null,
"cds_length": 2373,
"cds_start": 1877,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000449503.6",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1877A>G",
"hgvs_p": "p.Lys626Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000412945.2",
"strand": true,
"transcript": "ENST00000449503.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 778,
"aa_ref": "K",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4801,
"cdna_start": 3156,
"cds_end": null,
"cds_length": 2337,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000438794.6",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1991A>G",
"hgvs_p": "p.Lys664Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000391886.2",
"strand": true,
"transcript": "ENST00000438794.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 746,
"aa_ref": "K",
"aa_start": 585,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4685,
"cdna_start": 2393,
"cds_end": null,
"cds_length": 2241,
"cds_start": 1754,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000428312.6",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1754A>G",
"hgvs_p": "p.Lys585Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398661.2",
"strand": true,
"transcript": "ENST00000428312.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 432,
"aa_ref": "K",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1570,
"cdna_start": 813,
"cds_end": null,
"cds_length": 1299,
"cds_start": 812,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000416658.5",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.812A>G",
"hgvs_p": "p.Lys271Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389978.1",
"strand": true,
"transcript": "ENST00000416658.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 852,
"aa_ref": "K",
"aa_start": 688,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6312,
"cdna_start": 3201,
"cds_end": null,
"cds_length": 2559,
"cds_start": 2063,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_001377538.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Lys688Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364467.1",
"strand": true,
"transcript": "NM_001377538.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 852,
"aa_ref": "K",
"aa_start": 688,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5622,
"cdna_start": 3266,
"cds_end": null,
"cds_length": 2559,
"cds_start": 2063,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000705628.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Lys688Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516144.1",
"strand": true,
"transcript": "ENST00000705628.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 845,
"aa_ref": "K",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6291,
"cdna_start": 3180,
"cds_end": null,
"cds_length": 2538,
"cds_start": 2042,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_001377539.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.2042A>G",
"hgvs_p": "p.Lys681Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364468.1",
"strand": true,
"transcript": "NM_001377539.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 828,
"aa_ref": "K",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6240,
"cdna_start": 3129,
"cds_end": null,
"cds_length": 2487,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001304420.3",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1991A>G",
"hgvs_p": "p.Lys664Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001291349.1",
"strand": true,
"transcript": "NM_001304420.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 828,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6240,
"cdna_start": 3129,
"cds_end": null,
"cds_length": 2487,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
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"feature": "ENST00000659705.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1991A>G",
"hgvs_p": "p.Lys664Arg",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499241.1",
"strand": true,
"transcript": "ENST00000659705.1",
"transcript_support_level": null
},
{
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"aa_length": 825,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6330,
"cdna_start": 3129,
"cds_end": null,
"cds_length": 2478,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001377541.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1991A>G",
"hgvs_p": "p.Lys664Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364470.1",
"strand": true,
"transcript": "NM_001377541.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 825,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
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"cdna_start": 3129,
"cds_end": null,
"cds_length": 2478,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001377542.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1991A>G",
"hgvs_p": "p.Lys664Arg",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364471.1",
"strand": true,
"transcript": "NM_001377542.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 821,
"aa_ref": "K",
"aa_start": 660,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6318,
"cdna_start": 3117,
"cds_end": null,
"cds_length": 2466,
"cds_start": 1979,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001377545.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1979A>G",
"hgvs_p": "p.Lys660Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364474.1",
"strand": true,
"transcript": "NM_001377545.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 820,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5500,
"cdna_start": 3132,
"cds_end": null,
"cds_length": 2463,
"cds_start": 1967,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000705652.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1967A>G",
"hgvs_p": "p.Lys656Arg",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516151.1",
"strand": true,
"transcript": "ENST00000705652.1",
"transcript_support_level": null
},
{
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"aa_ref": "K",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 6189,
"cdna_start": 3078,
"cds_end": null,
"cds_length": 2436,
"cds_start": 1940,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_007159.5",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1940A>G",
"hgvs_p": "p.Lys647Arg",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_009090.2",
"strand": true,
"transcript": "NM_007159.5",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_start": 3157,
"cds_end": null,
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"cds_start": 1940,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000295951.7",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1940A>G",
"hgvs_p": "p.Lys647Arg",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000295951.3",
"strand": true,
"transcript": "ENST00000295951.7",
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},
{
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": 2145,
"cds_end": null,
"cds_length": 2436,
"cds_start": 1940,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000295952.7",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1940A>G",
"hgvs_p": "p.Lys647Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000295952.3",
"strand": true,
"transcript": "ENST00000295952.7",
"transcript_support_level": 2
},
{
"aa_alt": "R",
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"aa_length": 808,
"aa_ref": "K",
"aa_start": 647,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6279,
"cdna_start": 3078,
"cds_end": null,
"cds_length": 2427,
"cds_start": 1940,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001377549.1",
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"hgvs_c": "c.1940A>G",
"hgvs_p": "p.Lys647Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364478.1",
"strand": true,
"transcript": "NM_001377549.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 807,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
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"frequency_reference_population": 0.00038386424,
"gene_hgnc_id": 16643,
"gene_symbol": "SLMAP",
"gnomad_exomes_ac": 566,
"gnomad_exomes_af": 0.00039755,
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"gnomad_genomes_ac": 39,
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"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": "Brugada syndrome|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.222,
"pos": 57913179,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.061,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001377538.1"
}
]
}