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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: 19-46608584-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=46608584&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 46608584,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000291295.14",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.281A>C",
"hgvs_p": "p.Asp94Ala",
"transcript": "NM_005184.4",
"protein_id": "NP_005175.2",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 149,
"cds_start": 281,
"cds_end": null,
"cds_length": 450,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 2184,
"mane_select": "ENST00000291295.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.281A>C",
"hgvs_p": "p.Asp94Ala",
"transcript": "ENST00000291295.14",
"protein_id": "ENSP00000291295.8",
"transcript_support_level": 1,
"aa_start": 94,
"aa_end": null,
"aa_length": 149,
"cds_start": 281,
"cds_end": null,
"cds_length": 450,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 2184,
"mane_select": "NM_005184.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "ENST00000599839.5",
"protein_id": "ENSP00000471225.1",
"transcript_support_level": 1,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 1355,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.281A>C",
"hgvs_p": "p.Asp94Ala",
"transcript": "NM_001329922.1",
"protein_id": "NP_001316851.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 149,
"cds_start": 281,
"cds_end": null,
"cds_length": 450,
"cdna_start": 417,
"cdna_end": null,
"cdna_length": 2215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.281A>C",
"hgvs_p": "p.Asp94Ala",
"transcript": "ENST00000596362.1",
"protein_id": "ENSP00000472141.1",
"transcript_support_level": 2,
"aa_start": 94,
"aa_end": null,
"aa_length": 149,
"cds_start": 281,
"cds_end": null,
"cds_length": 450,
"cdna_start": 417,
"cdna_end": null,
"cdna_length": 1203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "NM_001329921.1",
"protein_id": "NP_001316850.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 2179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "NM_001329923.1",
"protein_id": "NP_001316852.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 2141,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "NM_001329924.2",
"protein_id": "NP_001316853.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 2182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "NM_001329925.2",
"protein_id": "NP_001316854.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "NM_001329926.2",
"protein_id": "NP_001316855.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 378,
"cdna_end": null,
"cdna_length": 2176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "ENST00000391918.6",
"protein_id": "ENSP00000375785.2",
"transcript_support_level": 2,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "ENST00000594523.5",
"protein_id": "ENSP00000468877.1",
"transcript_support_level": 4,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 342,
"cdna_end": null,
"cdna_length": 540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.173A>C",
"hgvs_p": "p.Asp58Ala",
"transcript": "ENST00000598871.5",
"protein_id": "ENSP00000470502.1",
"transcript_support_level": 4,
"aa_start": 58,
"aa_end": null,
"aa_length": 113,
"cds_start": 173,
"cds_end": null,
"cds_length": 342,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 561,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.405A>C",
"hgvs_p": null,
"transcript": "ENST00000477244.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 696,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.391A>C",
"hgvs_p": null,
"transcript": "ENST00000482455.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 650,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.482A>C",
"hgvs_p": null,
"transcript": "ENST00000486500.1",
"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": 2536,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.2710A>C",
"hgvs_p": null,
"transcript": "ENST00000595072.2",
"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": 2960,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.349A>C",
"hgvs_p": null,
"transcript": "ENST00000597868.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 927,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.*317A>C",
"hgvs_p": null,
"transcript": "ENST00000602169.2",
"protein_id": "ENSP00000499372.1",
"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": 880,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124904729",
"gene_hgnc_id": null,
"hgvs_c": "n.485T>G",
"hgvs_p": null,
"transcript": "XR_007067276.1",
"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": 1245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "n.*317A>C",
"hgvs_p": null,
"transcript": "ENST00000602169.2",
"protein_id": "ENSP00000499372.1",
"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": 880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"hgvs_c": "c.165+257A>C",
"hgvs_p": null,
"transcript": "ENST00000597743.5",
"protein_id": "ENSP00000470308.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 83,
"cds_start": -4,
"cds_end": null,
"cds_length": 252,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CALM3",
"gene_hgnc_id": 1449,
"dbsnp": "rs1060502608",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9999319314956665,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "CardioboostArm",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.91,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.213,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000291295.14",
"gene_symbol": "CALM3",
"hgnc_id": 1449,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.281A>C",
"hgvs_p": "p.Asp94Ala"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007067276.1",
"gene_symbol": "LOC124904729",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.485T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Long QT syndrome 1,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Long QT syndrome 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}