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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: 14-90404396-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=90404396&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CALM1",
"hgnc_id": 1442,
"hgvs_c": "c.306C>T",
"hgvs_p": "p.Ile102Ile",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_001363670.2",
"verdict": "Benign"
},
{
"benign_score": 14,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000258424",
"hgnc_id": null,
"hgvs_c": "n.44+796G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -14,
"transcript": "ENST00000555853.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_score": -14,
"allele_count_reference_population": 1709,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "14",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "CALM1-related disorder,Cardiovascular phenotype,Catecholaminergic polymorphic ventricular tachycardia 4,Long QT syndrome 14,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4300000071525574,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 149,
"aa_ref": "I",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4203,
"cdna_start": 505,
"cds_end": null,
"cds_length": 450,
"cds_start": 303,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_006888.6",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.303C>T",
"hgvs_p": "p.Ile101Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000356978.9",
"protein_coding": true,
"protein_id": "NP_008819.1",
"strand": true,
"transcript": "NM_006888.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 149,
"aa_ref": "I",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4203,
"cdna_start": 505,
"cds_end": null,
"cds_length": 450,
"cds_start": 303,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000356978.9",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.303C>T",
"hgvs_p": "p.Ile101Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006888.6",
"protein_coding": true,
"protein_id": "ENSP00000349467.4",
"strand": true,
"transcript": "ENST00000356978.9",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1064,
"cdna_start": 527,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000544280.6",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000442853.2",
"strand": true,
"transcript": "ENST00000544280.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2670,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000553964.5",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.2433C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000553964.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 156,
"aa_ref": "I",
"aa_start": 108,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 741,
"cdna_start": 526,
"cds_end": null,
"cds_length": 471,
"cds_start": 324,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000971957.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.324C>T",
"hgvs_p": "p.Ile108Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000642016.1",
"strand": true,
"transcript": "ENST00000971957.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 150,
"aa_ref": "I",
"aa_start": 102,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4919,
"cdna_start": 1221,
"cds_end": null,
"cds_length": 453,
"cds_start": 306,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001363670.2",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.306C>T",
"hgvs_p": "p.Ile102Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350599.1",
"strand": true,
"transcript": "NM_001363670.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4155,
"cdna_start": 457,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001363669.2",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350598.1",
"strand": true,
"transcript": "NM_001363669.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1104,
"cdna_start": 602,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000447653.8",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403491.4",
"strand": true,
"transcript": "ENST00000447653.8",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 877,
"cdna_start": 399,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000553542.5",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000450829.1",
"strand": true,
"transcript": "ENST00000553542.5",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 657,
"cdna_start": 467,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000659177.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499421.1",
"strand": true,
"transcript": "ENST00000659177.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 113,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 793,
"cdna_start": 398,
"cds_end": null,
"cds_length": 342,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000663135.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499498.1",
"strand": true,
"transcript": "ENST00000663135.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 97,
"aa_ref": "I",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 557,
"cdna_start": 457,
"cds_end": null,
"cds_length": 295,
"cds_start": 195,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000557020.5",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000451062.1",
"strand": true,
"transcript": "ENST00000557020.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1420,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000553630.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.196C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451646.1",
"strand": true,
"transcript": "ENST00000553630.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 531,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000554296.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.355C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000554296.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 444,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000556721.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.229C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000556721.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 438,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000553422.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.178-3C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000450425.1",
"strand": true,
"transcript": "ENST00000553422.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 300,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000555853.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258424",
"hgvs_c": "n.44+796G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000555853.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000555267.1",
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"hgvs_c": "n.*243C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000555267.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs143503733",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0010590857,
"gene_hgnc_id": 1442,
"gene_symbol": "CALM1",
"gnomad_exomes_ac": 1642,
"gnomad_exomes_af": 0.0011236,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 67,
"gnomad_genomes_af": 0.000439956,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Long QT syndrome 14;Catecholaminergic polymorphic ventricular tachycardia 4|Cardiovascular phenotype|not specified|not provided|CALM1-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.137,
"pos": 90404396,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001363670.2"
}
]
}