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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: 3-47123302-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=47123302&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SETD2",
"hgnc_id": 18420,
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445His",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_014159.7",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000296084",
"hgnc_id": null,
"hgvs_c": "n.236-994C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000736255.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.1998,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.26242175698280334,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2564,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8541,
"cdna_start": 1523,
"cds_end": null,
"cds_length": 7695,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_014159.7",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000409792.4",
"protein_coding": true,
"protein_id": "NP_054878.5",
"strand": false,
"transcript": "NM_014159.7",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2564,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8541,
"cdna_start": 1523,
"cds_end": null,
"cds_length": 7695,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000409792.4",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014159.7",
"protein_coding": true,
"protein_id": "ENSP00000386759.3",
"strand": false,
"transcript": "ENST00000409792.4",
"transcript_support_level": 5
},
{
"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": 8172,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000330022.11",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "n.947G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000332415.7",
"strand": false,
"transcript": "ENST00000330022.11",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2538,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8437,
"cdna_start": 1501,
"cds_end": null,
"cds_length": 7617,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000952253.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622312.1",
"strand": false,
"transcript": "ENST00000952253.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2520,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8525,
"cdna_start": 1507,
"cds_end": null,
"cds_length": 7563,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001349370.3",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001336299.1",
"strand": false,
"transcript": "NM_001349370.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2520,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8302,
"cdna_start": 1276,
"cds_end": null,
"cds_length": 7563,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000638947.2",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491413.2",
"strand": false,
"transcript": "ENST00000638947.2",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2486,
"aa_ref": "R",
"aa_start": 412,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8109,
"cdna_start": 1235,
"cds_end": null,
"cds_length": 7461,
"cds_start": 1235,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000685005.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1235G>A",
"hgvs_p": "p.Arg412His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509568.1",
"strand": false,
"transcript": "ENST00000685005.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1339,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4231,
"cdna_start": 1412,
"cds_end": null,
"cds_length": 4021,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000412450.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416401.1",
"strand": false,
"transcript": "ENST00000412450.1",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2520,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8322,
"cdna_start": 1304,
"cds_end": null,
"cds_length": 7563,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047448045.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304001.1",
"strand": false,
"transcript": "XM_047448045.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2475,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8187,
"cdna_start": 1304,
"cds_end": null,
"cds_length": 7428,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_024453487.2",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309255.1",
"strand": false,
"transcript": "XM_024453487.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2420,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7981,
"cdna_start": 1263,
"cds_end": null,
"cds_length": 7263,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_024453488.2",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309256.1",
"strand": false,
"transcript": "XM_024453488.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1633,
"aa_ref": "R",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5065,
"cdna_start": 1263,
"cds_end": null,
"cds_length": 4902,
"cds_start": 1202,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_024453489.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.1202G>A",
"hgvs_p": "p.Arg401His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309257.1",
"strand": false,
"transcript": "XM_024453489.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4140,
"cdna_start": null,
"cds_end": null,
"cds_length": 3312,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000893753.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.72-6548G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563812.1",
"strand": false,
"transcript": "ENST00000893753.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1059,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3980,
"cdna_start": null,
"cds_end": null,
"cds_length": 3180,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000952254.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.72-9298G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622313.1",
"strand": false,
"transcript": "ENST00000952254.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1016,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3792,
"cdna_start": null,
"cds_end": null,
"cds_length": 3051,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000952255.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.72-17182G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622314.1",
"strand": false,
"transcript": "ENST00000952255.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 916,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3416,
"cdna_start": null,
"cds_end": null,
"cds_length": 2751,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000691544.1",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "c.72-25221G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510710.1",
"strand": false,
"transcript": "ENST00000691544.1",
"transcript_support_level": null
},
{
"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": 7555,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000431180.5",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "n.485G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000388349.1",
"strand": false,
"transcript": "ENST00000431180.5",
"transcript_support_level": 2
},
{
"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": 7075,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000445387.5",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "n.233G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000411901.1",
"strand": false,
"transcript": "ENST00000445387.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 8709,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_146158.3",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "n.1523G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_146158.3",
"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": 6233,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XR_002959514.2",
"gene_hgnc_id": 18420,
"gene_symbol": "SETD2",
"hgvs_c": "n.1263G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_002959514.2",
"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": 7400,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
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