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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-124380579-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=124380579&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 124380579,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001163278.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8156A>G",
"hgvs_p": "p.Asn2719Ser",
"transcript": "NM_001163278.2",
"protein_id": "NP_001156750.1",
"transcript_support_level": null,
"aa_start": 2719,
"aa_end": null,
"aa_length": 2732,
"cds_start": 8156,
"cds_end": null,
"cds_length": 8199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000422452.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001163278.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8156A>G",
"hgvs_p": "p.Asn2719Ser",
"transcript": "ENST00000422452.4",
"protein_id": "ENSP00000403954.4",
"transcript_support_level": 1,
"aa_start": 2719,
"aa_end": null,
"aa_length": 2732,
"cds_start": 8156,
"cds_end": null,
"cds_length": 8199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001163278.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422452.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8135A>G",
"hgvs_p": "p.Asn2712Ser",
"transcript": "ENST00000371130.7",
"protein_id": "ENSP00000360171.3",
"transcript_support_level": 1,
"aa_start": 2712,
"aa_end": null,
"aa_length": 2725,
"cds_start": 8135,
"cds_end": null,
"cds_length": 8178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371130.7"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8153A>G",
"hgvs_p": "p.Asn2718Ser",
"transcript": "NM_001163279.1",
"protein_id": "NP_001156751.1",
"transcript_support_level": null,
"aa_start": 2718,
"aa_end": null,
"aa_length": 2731,
"cds_start": 8153,
"cds_end": null,
"cds_length": 8196,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001163279.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8135A>G",
"hgvs_p": "p.Asn2712Ser",
"transcript": "NM_014253.3",
"protein_id": "NP_055068.2",
"transcript_support_level": null,
"aa_start": 2712,
"aa_end": null,
"aa_length": 2725,
"cds_start": 8135,
"cds_end": null,
"cds_length": 8178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014253.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_017029208.3",
"protein_id": "XP_016884697.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029208.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_017029209.3",
"protein_id": "XP_016884698.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029209.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_017029210.3",
"protein_id": "XP_016884699.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029210.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_017029211.3",
"protein_id": "XP_016884700.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029211.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_017029213.3",
"protein_id": "XP_016884702.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029213.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8255A>G",
"hgvs_p": "p.Asn2752Ser",
"transcript": "XM_047441759.1",
"protein_id": "XP_047297715.1",
"transcript_support_level": null,
"aa_start": 2752,
"aa_end": null,
"aa_length": 2765,
"cds_start": 8255,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441759.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8135A>G",
"hgvs_p": "p.Asn2712Ser",
"transcript": "XM_017029214.3",
"protein_id": "XP_016884703.1",
"transcript_support_level": null,
"aa_start": 2712,
"aa_end": null,
"aa_length": 2725,
"cds_start": 8135,
"cds_end": null,
"cds_length": 8178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029214.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.8111A>G",
"hgvs_p": "p.Asn2704Ser",
"transcript": "XM_047441760.1",
"protein_id": "XP_047297716.1",
"transcript_support_level": null,
"aa_start": 2704,
"aa_end": null,
"aa_length": 2717,
"cds_start": 8111,
"cds_end": null,
"cds_length": 8154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441760.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.5861A>G",
"hgvs_p": "p.Asn1954Ser",
"transcript": "XM_011531236.4",
"protein_id": "XP_011529538.2",
"transcript_support_level": null,
"aa_start": 1954,
"aa_end": null,
"aa_length": 1967,
"cds_start": 5861,
"cds_end": null,
"cds_length": 5904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531236.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.4508A>G",
"hgvs_p": "p.Asn1503Ser",
"transcript": "XM_047441761.1",
"protein_id": "XP_047297717.1",
"transcript_support_level": null,
"aa_start": 1503,
"aa_end": null,
"aa_length": 1516,
"cds_start": 4508,
"cds_end": null,
"cds_length": 4551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441761.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.4409A>G",
"hgvs_p": "p.Asn1470Ser",
"transcript": "XM_047441762.1",
"protein_id": "XP_047297718.1",
"transcript_support_level": null,
"aa_start": 1470,
"aa_end": null,
"aa_length": 1483,
"cds_start": 4409,
"cds_end": null,
"cds_length": 4452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441762.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"hgvs_c": "c.4160A>G",
"hgvs_p": "p.Asn1387Ser",
"transcript": "XM_011531237.3",
"protein_id": "XP_011529539.1",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1400,
"cds_start": 4160,
"cds_end": null,
"cds_length": 4203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531237.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STAG2",
"gene_hgnc_id": 11355,
"hgvs_c": "n.454-31243T>C",
"hgvs_p": null,
"transcript": "ENST00000469481.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000469481.1"
}
],
"gene_symbol": "TENM1",
"gene_hgnc_id": 8117,
"dbsnp": "rs146419593",
"frequency_reference_population": 0.00031187644,
"hom_count_reference_population": 91,
"allele_count_reference_population": 377,
"gnomad_exomes_af": 0.000186016,
"gnomad_genomes_af": 0.0015428,
"gnomad_exomes_ac": 204,
"gnomad_genomes_ac": 173,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01032063364982605,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.23,
"revel_prediction": "Benign",
"alphamissense_score": 0.0622,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.1,
"phylop100way_prediction": "Uncertain_significance",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001163278.2",
"gene_symbol": "TENM1",
"hgnc_id": 8117,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.8156A>G",
"hgvs_p": "p.Asn2719Ser"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000469481.1",
"gene_symbol": "STAG2",
"hgnc_id": 11355,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "n.454-31243T>C",
"hgvs_p": null
}
],
"clinvar_disease": "TENM1-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "TENM1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}