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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: 13-101111178-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=101111178&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 101111178,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001350748.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2241C>T",
"hgvs_p": "p.Pro747Pro",
"transcript": "NM_052867.4",
"protein_id": "NP_443099.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1738,
"cds_start": 2241,
"cds_end": null,
"cds_length": 5217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000251127.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_052867.4"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2241C>T",
"hgvs_p": "p.Pro747Pro",
"transcript": "ENST00000251127.11",
"protein_id": "ENSP00000251127.6",
"transcript_support_level": 1,
"aa_start": 747,
"aa_end": null,
"aa_length": 1738,
"cds_start": 2241,
"cds_end": null,
"cds_length": 5217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_052867.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000251127.11"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2328C>T",
"hgvs_p": "p.Pro776Pro",
"transcript": "NM_001350748.2",
"protein_id": "NP_001337677.1",
"transcript_support_level": null,
"aa_start": 776,
"aa_end": null,
"aa_length": 1767,
"cds_start": 2328,
"cds_end": null,
"cds_length": 5304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350748.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2328C>T",
"hgvs_p": "p.Pro776Pro",
"transcript": "ENST00000675332.1",
"protein_id": "ENSP00000501955.1",
"transcript_support_level": null,
"aa_start": 776,
"aa_end": null,
"aa_length": 1767,
"cds_start": 2328,
"cds_end": null,
"cds_length": 5304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675332.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2241C>T",
"hgvs_p": "p.Pro747Pro",
"transcript": "NM_001350749.2",
"protein_id": "NP_001337678.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1738,
"cds_start": 2241,
"cds_end": null,
"cds_length": 5217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350749.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2241C>T",
"hgvs_p": "p.Pro747Pro",
"transcript": "ENST00000858715.1",
"protein_id": "ENSP00000528774.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1738,
"cds_start": 2241,
"cds_end": null,
"cds_length": 5217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858715.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2157C>T",
"hgvs_p": "p.Pro719Pro",
"transcript": "ENST00000949519.1",
"protein_id": "ENSP00000619578.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1710,
"cds_start": 2157,
"cds_end": null,
"cds_length": 5133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949519.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2154C>T",
"hgvs_p": "p.Pro718Pro",
"transcript": "NM_001350750.2",
"protein_id": "NP_001337679.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1709,
"cds_start": 2154,
"cds_end": null,
"cds_length": 5130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350750.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2154C>T",
"hgvs_p": "p.Pro718Pro",
"transcript": "NM_001350751.2",
"protein_id": "NP_001337680.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1709,
"cds_start": 2154,
"cds_end": null,
"cds_length": 5130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350751.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2154C>T",
"hgvs_p": "p.Pro718Pro",
"transcript": "ENST00000676315.1",
"protein_id": "ENSP00000501603.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1709,
"cds_start": 2154,
"cds_end": null,
"cds_length": 5130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676315.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2049C>T",
"hgvs_p": "p.Pro683Pro",
"transcript": "ENST00000949518.1",
"protein_id": "ENSP00000619577.1",
"transcript_support_level": null,
"aa_start": 683,
"aa_end": null,
"aa_length": 1674,
"cds_start": 2049,
"cds_end": null,
"cds_length": 5025,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949518.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.1962C>T",
"hgvs_p": "p.Pro654Pro",
"transcript": "ENST00000675150.1",
"protein_id": "ENSP00000502680.1",
"transcript_support_level": null,
"aa_start": 654,
"aa_end": null,
"aa_length": 1645,
"cds_start": 1962,
"cds_end": null,
"cds_length": 4938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675150.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2385C>T",
"hgvs_p": "p.Pro795Pro",
"transcript": "XM_024449336.2",
"protein_id": "XP_024305104.1",
"transcript_support_level": null,
"aa_start": 795,
"aa_end": null,
"aa_length": 1786,
"cds_start": 2385,
"cds_end": null,
"cds_length": 5361,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024449336.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2298C>T",
"hgvs_p": "p.Pro766Pro",
"transcript": "XM_011521067.3",
"protein_id": "XP_011519369.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 1757,
"cds_start": 2298,
"cds_end": null,
"cds_length": 5274,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521067.3"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2211C>T",
"hgvs_p": "p.Pro737Pro",
"transcript": "XM_011521069.3",
"protein_id": "XP_011519371.1",
"transcript_support_level": null,
"aa_start": 737,
"aa_end": null,
"aa_length": 1728,
"cds_start": 2211,
"cds_end": null,
"cds_length": 5187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521069.3"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.1794C>T",
"hgvs_p": "p.Pro598Pro",
"transcript": "XM_017020536.3",
"protein_id": "XP_016876025.1",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 1589,
"cds_start": 1794,
"cds_end": null,
"cds_length": 4770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020536.3"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.1476C>T",
"hgvs_p": "p.Pro492Pro",
"transcript": "XM_017020537.2",
"protein_id": "XP_016876026.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 1483,
"cds_start": 1476,
"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_017020537.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "n.2241C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000648359.1"
}
],
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"dbsnp": "rs79264337",
"frequency_reference_population": 0.0037139591,
"hom_count_reference_population": 12,
"allele_count_reference_population": 5974,
"gnomad_exomes_af": 0.00358633,
"gnomad_genomes_af": 0.00493546,
"gnomad_exomes_ac": 5223,
"gnomad_genomes_ac": 751,
"gnomad_exomes_homalt": 10,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.834,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001350748.2",
"gene_symbol": "NALCN",
"hgnc_id": 19082,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2328C>T",
"hgvs_p": "p.Pro776Pro"
}
],
"clinvar_disease": " and developmental delay, hypotonia, infantile, with psychomotor retardation and characteristic facies 1,Congenital contractures of the limbs and face,Hypotonia,NALCN-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay;Hypotonia, infantile, with psychomotor retardation and characteristic facies 1|NALCN-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}