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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: 13-101095574-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=101095574&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 101095574,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000251127.11",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3269G>A",
"hgvs_p": "p.Trp1090*",
"transcript": "NM_052867.4",
"protein_id": "NP_443099.1",
"transcript_support_level": null,
"aa_start": 1090,
"aa_end": null,
"aa_length": 1738,
"cds_start": 3269,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 3504,
"cdna_end": null,
"cdna_length": 6971,
"mane_select": "ENST00000251127.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3269G>A",
"hgvs_p": "p.Trp1090*",
"transcript": "ENST00000251127.11",
"protein_id": "ENSP00000251127.6",
"transcript_support_level": 1,
"aa_start": 1090,
"aa_end": null,
"aa_length": 1738,
"cds_start": 3269,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 3504,
"cdna_end": null,
"cdna_length": 6971,
"mane_select": "NM_052867.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3356G>A",
"hgvs_p": "p.Trp1119*",
"transcript": "NM_001350748.2",
"protein_id": "NP_001337677.1",
"transcript_support_level": null,
"aa_start": 1119,
"aa_end": null,
"aa_length": 1767,
"cds_start": 3356,
"cds_end": null,
"cds_length": 5304,
"cdna_start": 3591,
"cdna_end": null,
"cdna_length": 7058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3356G>A",
"hgvs_p": "p.Trp1119*",
"transcript": "ENST00000675332.1",
"protein_id": "ENSP00000501955.1",
"transcript_support_level": null,
"aa_start": 1119,
"aa_end": null,
"aa_length": 1767,
"cds_start": 3356,
"cds_end": null,
"cds_length": 5304,
"cdna_start": 3530,
"cdna_end": null,
"cdna_length": 6958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3269G>A",
"hgvs_p": "p.Trp1090*",
"transcript": "NM_001350749.2",
"protein_id": "NP_001337678.1",
"transcript_support_level": null,
"aa_start": 1090,
"aa_end": null,
"aa_length": 1738,
"cds_start": 3269,
"cds_end": null,
"cds_length": 5217,
"cdna_start": 3381,
"cdna_end": null,
"cdna_length": 6848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3182G>A",
"hgvs_p": "p.Trp1061*",
"transcript": "NM_001350750.2",
"protein_id": "NP_001337679.1",
"transcript_support_level": null,
"aa_start": 1061,
"aa_end": null,
"aa_length": 1709,
"cds_start": 3182,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 3417,
"cdna_end": null,
"cdna_length": 6884,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3182G>A",
"hgvs_p": "p.Trp1061*",
"transcript": "NM_001350751.2",
"protein_id": "NP_001337680.1",
"transcript_support_level": null,
"aa_start": 1061,
"aa_end": null,
"aa_length": 1709,
"cds_start": 3182,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 3294,
"cdna_end": null,
"cdna_length": 6761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3182G>A",
"hgvs_p": "p.Trp1061*",
"transcript": "ENST00000676315.1",
"protein_id": "ENSP00000501603.1",
"transcript_support_level": null,
"aa_start": 1061,
"aa_end": null,
"aa_length": 1709,
"cds_start": 3182,
"cds_end": null,
"cds_length": 5130,
"cdna_start": 3383,
"cdna_end": null,
"cdna_length": 6842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2990G>A",
"hgvs_p": "p.Trp997*",
"transcript": "ENST00000675150.1",
"protein_id": "ENSP00000502680.1",
"transcript_support_level": null,
"aa_start": 997,
"aa_end": null,
"aa_length": 1645,
"cds_start": 2990,
"cds_end": null,
"cds_length": 4938,
"cdna_start": 3088,
"cdna_end": null,
"cdna_length": 6548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3413G>A",
"hgvs_p": "p.Trp1138*",
"transcript": "XM_024449336.2",
"protein_id": "XP_024305104.1",
"transcript_support_level": null,
"aa_start": 1138,
"aa_end": null,
"aa_length": 1786,
"cds_start": 3413,
"cds_end": null,
"cds_length": 5361,
"cdna_start": 3458,
"cdna_end": null,
"cdna_length": 6925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3326G>A",
"hgvs_p": "p.Trp1109*",
"transcript": "XM_011521067.3",
"protein_id": "XP_011519369.1",
"transcript_support_level": null,
"aa_start": 1109,
"aa_end": null,
"aa_length": 1757,
"cds_start": 3326,
"cds_end": null,
"cds_length": 5274,
"cdna_start": 3371,
"cdna_end": null,
"cdna_length": 6838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.3239G>A",
"hgvs_p": "p.Trp1080*",
"transcript": "XM_011521069.3",
"protein_id": "XP_011519371.1",
"transcript_support_level": null,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1728,
"cds_start": 3239,
"cds_end": null,
"cds_length": 5187,
"cdna_start": 3284,
"cdna_end": null,
"cdna_length": 6751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2822G>A",
"hgvs_p": "p.Trp941*",
"transcript": "XM_017020536.3",
"protein_id": "XP_016876025.1",
"transcript_support_level": null,
"aa_start": 941,
"aa_end": null,
"aa_length": 1589,
"cds_start": 2822,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 3207,
"cdna_end": null,
"cdna_length": 6674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "c.2504G>A",
"hgvs_p": "p.Trp835*",
"transcript": "XM_017020537.2",
"protein_id": "XP_016876026.1",
"transcript_support_level": null,
"aa_start": 835,
"aa_end": null,
"aa_length": 1483,
"cds_start": 2504,
"cds_end": null,
"cds_length": 4452,
"cdna_start": 2599,
"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": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"hgvs_c": "n.3269G>A",
"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
}
],
"gene_symbol": "NALCN",
"gene_hgnc_id": 19082,
"dbsnp": "rs1555379886",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.984000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.418,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.31,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999914581504043,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1",
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000251127.11",
"gene_symbol": "NALCN",
"hgnc_id": 19082,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3269G>A",
"hgvs_p": "p.Trp1090*"
}
],
"clinvar_disease": " infantile, with psychomotor retardation and characteristic facies 1,Hypotonia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}