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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: X-5903781-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=5903781&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 5903781,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000381095.8",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_181332.3",
"protein_id": "NP_851849.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1529,
"cdna_end": null,
"cdna_length": 5858,
"mane_select": "ENST00000381095.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "ENST00000381095.8",
"protein_id": "ENSP00000370485.3",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1529,
"cdna_end": null,
"cdna_length": 5858,
"mane_select": "NM_181332.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "ENST00000538097.6",
"protein_id": "ENSP00000439203.3",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 836,
"cds_start": 957,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 3124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "ENST00000275857.10",
"protein_id": "ENSP00000275857.6",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 5454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001282145.2",
"protein_id": "NP_001269074.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 6165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001282146.2",
"protein_id": "NP_001269075.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1410,
"cdna_end": null,
"cdna_length": 5739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001441322.1",
"protein_id": "NP_001428251.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 5753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001441323.1",
"protein_id": "NP_001428252.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 5601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001441324.1",
"protein_id": "NP_001428253.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1597,
"cdna_end": null,
"cdna_length": 5926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_001441325.1",
"protein_id": "NP_001428254.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 5931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "NM_020742.4",
"protein_id": "NP_065793.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 5690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "ENST00000381092.1",
"protein_id": "ENSP00000370482.1",
"transcript_support_level": 2,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 3750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "ENST00000381093.6",
"protein_id": "ENSP00000370483.3",
"transcript_support_level": 2,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1526,
"cdna_end": null,
"cdna_length": 5865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_005274564.4",
"protein_id": "XP_005274621.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_005274565.3",
"protein_id": "XP_005274622.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 836,
"cds_start": 957,
"cds_end": null,
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"cdna_start": 1470,
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"cdna_length": 5799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_005274566.5",
"protein_id": "XP_005274623.1",
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_006724504.3",
"protein_id": "XP_006724567.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 836,
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"cdna_start": 1466,
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"cdna_length": 5795,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_011545547.3",
"protein_id": "XP_011543849.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 836,
"cds_start": 957,
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"cdna_start": 1484,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 6,
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"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.957A>G",
"hgvs_p": "p.Ile319Met",
"transcript": "XM_011545548.3",
"protein_id": "XP_011543850.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "XM_017029693.2",
"protein_id": "XP_016885182.1",
"transcript_support_level": null,
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"aa_end": null,
"aa_length": 816,
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"cdna_start": 1652,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 6,
"intron_rank": null,
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"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "XM_047442281.1",
"protein_id": "XP_047298237.1",
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"aa_start": 299,
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"cdna_start": 1651,
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"cdna_length": 5980,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "NLGN4X",
"gene_hgnc_id": 14287,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "XM_047442282.1",
"protein_id": "XP_047298238.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 816,
"cds_start": 897,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1497,
"cdna_end": null,
"cdna_length": 5826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NLGN4X",
"gene_hgnc_id": 14287,
"dbsnp": "rs151073358",
"frequency_reference_population": 0.0012386823,
"hom_count_reference_population": 387,
"allele_count_reference_population": 1499,
"gnomad_exomes_af": 0.000664693,
"gnomad_genomes_af": 0.00687184,
"gnomad_exomes_ac": 730,
"gnomad_genomes_ac": 769,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 8,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004701137542724609,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.031,
"revel_prediction": "Benign",
"alphamissense_score": 0.0483,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.051,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000381095.8",
"gene_symbol": "NLGN4X",
"hgnc_id": 14287,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}