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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: 9-69216367-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=69216367&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 69216367,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000377245.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "NM_004817.4",
"protein_id": "NP_004808.2",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 1190,
"cds_start": 143,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 4503,
"mane_select": "ENST00000377245.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "ENST00000377245.9",
"protein_id": "ENSP00000366453.4",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 1190,
"cds_start": 143,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 4503,
"mane_select": "NM_004817.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "c.530T>C",
"hgvs_p": "p.Val177Ala",
"transcript": "ENST00000642889.1",
"protein_id": "ENSP00000493780.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 1319,
"cds_start": 530,
"cds_end": null,
"cds_length": 3960,
"cdna_start": 563,
"cdna_end": null,
"cdna_length": 4806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "ENST00000348208.9",
"protein_id": "ENSP00000345893.4",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 1043,
"cds_start": 143,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 4055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "n.222T>C",
"hgvs_p": null,
"transcript": "ENST00000636247.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 3725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.320T>C",
"hgvs_p": "p.Val107Ala",
"transcript": "ENST00000636438.1",
"protein_id": "ENSP00000489860.1",
"transcript_support_level": 5,
"aa_start": 107,
"aa_end": null,
"aa_length": 1249,
"cds_start": 320,
"cds_end": null,
"cds_length": 3750,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 4689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.236T>C",
"hgvs_p": "p.Val79Ala",
"transcript": "NM_001170416.2",
"protein_id": "NP_001163887.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 1221,
"cds_start": 236,
"cds_end": null,
"cds_length": 3666,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 4503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.236T>C",
"hgvs_p": "p.Val79Ala",
"transcript": "ENST00000539225.2",
"protein_id": "ENSP00000438262.1",
"transcript_support_level": 2,
"aa_start": 79,
"aa_end": null,
"aa_length": 1221,
"cds_start": 236,
"cds_end": null,
"cds_length": 3666,
"cdna_start": 236,
"cdna_end": null,
"cdna_length": 3838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Val52Ala",
"transcript": "NM_001369875.1",
"protein_id": "NP_001356804.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 1194,
"cds_start": 155,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 4422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.146T>C",
"hgvs_p": "p.Val49Ala",
"transcript": "ENST00000650084.1",
"protein_id": "ENSP00000497861.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 1191,
"cds_start": 146,
"cds_end": null,
"cds_length": 3576,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 4389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.74T>C",
"hgvs_p": "p.Val25Ala",
"transcript": "NM_001369871.1",
"protein_id": "NP_001356800.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 1167,
"cds_start": 74,
"cds_end": null,
"cds_length": 3504,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 4681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.74T>C",
"hgvs_p": "p.Val25Ala",
"transcript": "NM_001369870.1",
"protein_id": "NP_001356799.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 1165,
"cds_start": 74,
"cds_end": null,
"cds_length": 3498,
"cdna_start": 431,
"cdna_end": null,
"cdna_length": 4685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Val52Ala",
"transcript": "NM_001170415.1",
"protein_id": "NP_001163886.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 1157,
"cds_start": 155,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 306,
"cdna_end": null,
"cdna_length": 4459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Val52Ala",
"transcript": "ENST00000535702.6",
"protein_id": "ENSP00000442090.1",
"transcript_support_level": 2,
"aa_start": 52,
"aa_end": null,
"aa_length": 1157,
"cds_start": 155,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 3984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "NM_001369872.1",
"protein_id": "NP_001356801.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 1153,
"cds_start": 143,
"cds_end": null,
"cds_length": 3462,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 4388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.74T>C",
"hgvs_p": "p.Val25Ala",
"transcript": "ENST00000650333.1",
"protein_id": "ENSP00000496791.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 1128,
"cds_start": 74,
"cds_end": null,
"cds_length": 3387,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 3612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "ENST00000649943.1",
"protein_id": "ENSP00000497539.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 1099,
"cds_start": 143,
"cds_end": null,
"cds_length": 3300,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 5672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "NM_001369873.1",
"protein_id": "NP_001356802.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 1082,
"cds_start": 143,
"cds_end": null,
"cds_length": 3249,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 4175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Val52Ala",
"transcript": "NM_001369874.1",
"protein_id": "NP_001356803.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 1047,
"cds_start": 155,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Val52Ala",
"transcript": "ENST00000649134.1",
"protein_id": "ENSP00000498068.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 1047,
"cds_start": 155,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 3964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "NM_201629.3",
"protein_id": "NP_963923.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 1043,
"cds_start": 143,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 4284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.74T>C",
"hgvs_p": "p.Val25Ala",
"transcript": "NM_001170414.2",
"protein_id": "NP_001163885.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 1020,
"cds_start": 74,
"cds_end": null,
"cds_length": 3063,
"cdna_start": 306,
"cdna_end": null,
"cdna_length": 4129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala",
"transcript": "ENST00000649114.1",
"protein_id": "ENSP00000497328.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
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"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TJP2",
"gene_hgnc_id": 11828,
"dbsnp": "rs121918299",
"frequency_reference_population": 0.000047706082,
"hom_count_reference_population": 5,
"allele_count_reference_population": 77,
"gnomad_exomes_af": 6.84059e-7,
"gnomad_genomes_af": 0.000499382,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 76,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.459952712059021,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.637,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9598,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.893,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP5_Very_Strong,BS2_Supporting",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 1,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BS2_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000377245.9",
"gene_symbol": "TJP2",
"hgnc_id": 11828,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Val48Ala"
},
{
"score": 4,
"benign_score": 4,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000642889.1",
"gene_symbol": "ENSG00000285130",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.530T>C",
"hgvs_p": "p.Val177Ala"
}
],
"clinvar_disease": " 4, familial 1, progressive familial intrahepatic,Cholestasis,Hypercholanemia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Hypercholanemia, familial 1|Cholestasis, progressive familial intrahepatic, 4|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}