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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: 15-100574025-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=100574025&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 100574025,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000314742.13",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "NM_001040616.3",
"protein_id": "NP_001035706.2",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 757,
"cds_start": 848,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": "ENST00000314742.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "ENST00000314742.13",
"protein_id": "ENSP00000318423.8",
"transcript_support_level": 5,
"aa_start": 283,
"aa_end": null,
"aa_length": 757,
"cds_start": 848,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": "NM_001040616.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "ENST00000561308.5",
"protein_id": "ENSP00000454200.1",
"transcript_support_level": 1,
"aa_start": 283,
"aa_end": null,
"aa_length": 436,
"cds_start": 848,
"cds_end": null,
"cds_length": 1311,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 1612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.803T>A",
"hgvs_p": "p.Met268Lys",
"transcript": "NM_001352508.2",
"protein_id": "NP_001339437.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 706,
"cds_start": 803,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 970,
"cdna_end": null,
"cdna_length": 4602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.101T>A",
"hgvs_p": "p.Met34Lys",
"transcript": "NM_001352507.2",
"protein_id": "NP_001339436.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 508,
"cds_start": 101,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1177,
"cdna_end": null,
"cdna_length": 4917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.491T>A",
"hgvs_p": "p.Met164Lys",
"transcript": "ENST00000560133.5",
"protein_id": "ENSP00000454929.1",
"transcript_support_level": 2,
"aa_start": 164,
"aa_end": null,
"aa_length": 317,
"cds_start": 491,
"cds_end": null,
"cds_length": 954,
"cdna_start": 648,
"cdna_end": null,
"cdna_length": 1196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_005254941.3",
"protein_id": "XP_005254998.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 757,
"cds_start": 848,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 4759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_024449980.2",
"protein_id": "XP_024305748.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 757,
"cds_start": 848,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1904,
"cdna_end": null,
"cdna_length": 5644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_005254943.3",
"protein_id": "XP_005255000.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 721,
"cds_start": 848,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 4647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_047432784.1",
"protein_id": "XP_047288740.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 721,
"cds_start": 848,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 4651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_047432785.1",
"protein_id": "XP_047288741.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 721,
"cds_start": 848,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1904,
"cdna_end": null,
"cdna_length": 5536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.101T>A",
"hgvs_p": "p.Met34Lys",
"transcript": "XM_017022399.3",
"protein_id": "XP_016877888.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 508,
"cds_start": 101,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 4121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"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": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_047432786.1",
"protein_id": "XP_047288742.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 409,
"cds_start": 848,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 2488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "K",
"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": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys",
"transcript": "XM_047432787.1",
"protein_id": "XP_047288743.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 409,
"cds_start": 848,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 1904,
"cdna_end": null,
"cdna_length": 3377,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1005T>A",
"hgvs_p": null,
"transcript": "ENST00000559149.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1015T>A",
"hgvs_p": null,
"transcript": "NR_148017.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 4711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1015T>A",
"hgvs_p": null,
"transcript": "NR_148018.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1019T>A",
"hgvs_p": null,
"transcript": "NR_148019.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1015T>A",
"hgvs_p": null,
"transcript": "XR_007064471.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.1015T>A",
"hgvs_p": null,
"transcript": "XR_007064472.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.-185T>A",
"hgvs_p": null,
"transcript": "ENST00000560783.1",
"protein_id": "ENSP00000474128.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.*208T>A",
"hgvs_p": null,
"transcript": "ENST00000560941.5",
"protein_id": "ENSP00000454985.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": -4,
"cds_end": null,
"cds_length": 397,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"dbsnp": "rs780141210",
"frequency_reference_population": 0.000012392065,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000109462,
"gnomad_genomes_af": 0.0000262733,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20416447520256042,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.074,
"revel_prediction": "Benign",
"alphamissense_score": 0.4814,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.888,
"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": "ENST00000314742.13",
"gene_symbol": "LINS1",
"hgnc_id": 30922,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.848T>A",
"hgvs_p": "p.Met283Lys"
}
],
"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
}