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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: 13-101057985-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=101057985&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 101057985,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000251127.11",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4977C>G",
"hgvs_p": "p.Asp1659Glu",
"transcript": "NM_052867.4",
"protein_id": "NP_443099.1",
"transcript_support_level": null,
"aa_start": 1659,
"aa_end": null,
"aa_length": 1738,
"cds_start": 4977,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 5212,
"cdna_end": null,
"cdna_length": 6971,
"mane_select": "ENST00000251127.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4977C>G",
"hgvs_p": "p.Asp1659Glu",
"transcript": "ENST00000251127.11",
"protein_id": "ENSP00000251127.6",
"transcript_support_level": 1,
"aa_start": 1659,
"aa_end": null,
"aa_length": 1738,
"cds_start": 4977,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 5212,
"cdna_end": null,
"cdna_length": 6971,
"mane_select": "NM_052867.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.5064C>G",
"hgvs_p": "p.Asp1688Glu",
"transcript": "NM_001350748.2",
"protein_id": "NP_001337677.1",
"transcript_support_level": null,
"aa_start": 1688,
"aa_end": null,
"aa_length": 1767,
"cds_start": 5064,
"cds_end": null,
"cds_length": 5304,
"cdna_start": 5299,
"cdna_end": null,
"cdna_length": 7058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.5064C>G",
"hgvs_p": "p.Asp1688Glu",
"transcript": "ENST00000675332.1",
"protein_id": "ENSP00000501955.1",
"transcript_support_level": null,
"aa_start": 1688,
"aa_end": null,
"aa_length": 1767,
"cds_start": 5064,
"cds_end": null,
"cds_length": 5304,
"cdna_start": 5238,
"cdna_end": null,
"cdna_length": 6958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4977C>G",
"hgvs_p": "p.Asp1659Glu",
"transcript": "NM_001350749.2",
"protein_id": "NP_001337678.1",
"transcript_support_level": null,
"aa_start": 1659,
"aa_end": null,
"aa_length": 1738,
"cds_start": 4977,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 5089,
"cdna_end": null,
"cdna_length": 6848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4890C>G",
"hgvs_p": "p.Asp1630Glu",
"transcript": "NM_001350750.2",
"protein_id": "NP_001337679.1",
"transcript_support_level": null,
"aa_start": 1630,
"aa_end": null,
"aa_length": 1709,
"cds_start": 4890,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 5125,
"cdna_end": null,
"cdna_length": 6884,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4890C>G",
"hgvs_p": "p.Asp1630Glu",
"transcript": "NM_001350751.2",
"protein_id": "NP_001337680.1",
"transcript_support_level": null,
"aa_start": 1630,
"aa_end": null,
"aa_length": 1709,
"cds_start": 4890,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 5002,
"cdna_end": null,
"cdna_length": 6761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4890C>G",
"hgvs_p": "p.Asp1630Glu",
"transcript": "ENST00000676315.1",
"protein_id": "ENSP00000501603.1",
"transcript_support_level": null,
"aa_start": 1630,
"aa_end": null,
"aa_length": 1709,
"cds_start": 4890,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 5091,
"cdna_end": null,
"cdna_length": 6842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4698C>G",
"hgvs_p": "p.Asp1566Glu",
"transcript": "ENST00000675150.1",
"protein_id": "ENSP00000502680.1",
"transcript_support_level": null,
"aa_start": 1566,
"aa_end": null,
"aa_length": 1645,
"cds_start": 4698,
"cds_end": null,
"cds_length": 4938,
"cdna_start": 4796,
"cdna_end": null,
"cdna_length": 6548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.5121C>G",
"hgvs_p": "p.Asp1707Glu",
"transcript": "XM_024449336.2",
"protein_id": "XP_024305104.1",
"transcript_support_level": null,
"aa_start": 1707,
"aa_end": null,
"aa_length": 1786,
"cds_start": 5121,
"cds_end": null,
"cds_length": 5361,
"cdna_start": 5166,
"cdna_end": null,
"cdna_length": 6925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.5034C>G",
"hgvs_p": "p.Asp1678Glu",
"transcript": "XM_011521067.3",
"protein_id": "XP_011519369.1",
"transcript_support_level": null,
"aa_start": 1678,
"aa_end": null,
"aa_length": 1757,
"cds_start": 5034,
"cds_end": null,
"cds_length": 5274,
"cdna_start": 5079,
"cdna_end": null,
"cdna_length": 6838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4947C>G",
"hgvs_p": "p.Asp1649Glu",
"transcript": "XM_011521069.3",
"protein_id": "XP_011519371.1",
"transcript_support_level": null,
"aa_start": 1649,
"aa_end": null,
"aa_length": 1728,
"cds_start": 4947,
"cds_end": null,
"cds_length": 5187,
"cdna_start": 4992,
"cdna_end": null,
"cdna_length": 6751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4530C>G",
"hgvs_p": "p.Asp1510Glu",
"transcript": "XM_017020536.3",
"protein_id": "XP_016876025.1",
"transcript_support_level": null,
"aa_start": 1510,
"aa_end": null,
"aa_length": 1589,
"cds_start": 4530,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 4915,
"cdna_end": null,
"cdna_length": 6674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.4212C>G",
"hgvs_p": "p.Asp1404Glu",
"transcript": "XM_017020537.2",
"protein_id": "XP_016876026.1",
"transcript_support_level": null,
"aa_start": 1404,
"aa_end": null,
"aa_length": 1483,
"cds_start": 4212,
"cds_end": null,
"cds_length": 4452,
"cdna_start": 4307,
"cdna_end": null,
"cdna_length": 6066,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN-AS1",
"gene_hgnc_id": 42743,
"hgvs_c": "n.1545G>C",
"hgvs_p": null,
"transcript": "ENST00000457843.1",
"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": 2846,
"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": 44,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "n.*597C>G",
"hgvs_p": null,
"transcript": "ENST00000648359.1",
"protein_id": "ENSP00000497465.1",
"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": 7105,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN-AS1",
"gene_hgnc_id": 42743,
"hgvs_c": "n.1545G>C",
"hgvs_p": null,
"transcript": "NR_047687.1",
"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": 2846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "n.*597C>G",
"hgvs_p": null,
"transcript": "ENST00000648359.1",
"protein_id": "ENSP00000497465.1",
"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": 7105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "NALCN-AS1",
"gene_hgnc_id": 42743,
"hgvs_c": "n.206+8620G>C",
"hgvs_p": null,
"transcript": "ENST00000787138.1",
"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": 482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"dbsnp": "rs78817184",
"frequency_reference_population": 0.00029988796,
"hom_count_reference_population": 1,
"allele_count_reference_population": 484,
"gnomad_exomes_af": 0.000177197,
"gnomad_genomes_af": 0.00147744,
"gnomad_exomes_ac": 259,
"gnomad_genomes_ac": 225,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005455642938613892,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.285,
"revel_prediction": "Benign",
"alphamissense_score": 0.0911,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.091,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000251127.11",
"gene_symbol": "NALCN",
"hgnc_id": 19082,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4977C>G",
"hgvs_p": "p.Asp1659Glu"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000457843.1",
"gene_symbol": "NALCN-AS1",
"hgnc_id": 42743,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1545G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,NALCN-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "not provided|Inborn genetic diseases|NALCN-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}