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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: 4-47949894-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=47949894&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 47949894,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000514170.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "NM_001379270.1",
"protein_id": "NP_001366199.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 2926,
"mane_select": "ENST00000514170.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000514170.7",
"protein_id": "ENSP00000426862.3",
"transcript_support_level": 5,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 2926,
"mane_select": "NM_001379270.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000402813.9",
"protein_id": "ENSP00000384264.5",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 588,
"cdna_end": null,
"cdna_length": 2867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "NM_000087.5",
"protein_id": "NP_000078.3",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 505,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "NM_001142564.2",
"protein_id": "NP_001136036.2",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 588,
"cdna_end": null,
"cdna_length": 2867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000420489.7",
"protein_id": "ENSP00000389881.3",
"transcript_support_level": 2,
"aa_start": 76,
"aa_end": null,
"aa_length": 686,
"cds_start": 226,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 2746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000504722.6",
"protein_id": "ENSP00000423721.2",
"transcript_support_level": 4,
"aa_start": 76,
"aa_end": null,
"aa_length": 123,
"cds_start": 226,
"cds_end": null,
"cds_length": 373,
"cdna_start": 396,
"cdna_end": null,
"cdna_length": 543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000514520.6",
"protein_id": "ENSP00000421110.2",
"transcript_support_level": 2,
"aa_start": 76,
"aa_end": null,
"aa_length": 94,
"cds_start": 226,
"cds_end": null,
"cds_length": 287,
"cdna_start": 344,
"cdna_end": null,
"cdna_length": 405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys",
"transcript": "ENST00000513178.2",
"protein_id": "ENSP00000423327.2",
"transcript_support_level": 3,
"aa_start": 76,
"aa_end": null,
"aa_length": 94,
"cds_start": 226,
"cds_end": null,
"cds_length": 285,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.238G>A",
"hgvs_p": "p.Glu80Lys",
"transcript": "XM_005248049.5",
"protein_id": "XP_005248106.3",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 690,
"cds_start": 238,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 2718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "c.238G>A",
"hgvs_p": "p.Glu80Lys",
"transcript": "XM_011513623.3",
"protein_id": "XP_011511925.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 690,
"cds_start": 238,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 2818,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"hgvs_c": "n.226G>A",
"hgvs_p": null,
"transcript": "ENST00000506118.1",
"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": 701,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NIPAL1",
"gene_hgnc_id": 27194,
"hgvs_c": "n.479-9130C>T",
"hgvs_p": null,
"transcript": "ENST00000500571.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 596,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NIPAL1",
"gene_hgnc_id": 27194,
"hgvs_c": "n.563+35190C>T",
"hgvs_p": null,
"transcript": "ENST00000513724.1",
"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": 690,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC101927157",
"gene_hgnc_id": null,
"hgvs_c": "n.479-9130C>T",
"hgvs_p": null,
"transcript": "NR_125879.1",
"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": 1666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CNGA1",
"gene_hgnc_id": 2148,
"dbsnp": "rs121909599",
"frequency_reference_population": 0.0000027367419,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273674,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.029313385486602783,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.014000000432133675,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0928,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.109,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.17,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000956780589783037,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000514170.7",
"gene_symbol": "CNGA1",
"hgnc_id": 2148,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Glu76Lys"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000513724.1",
"gene_symbol": "NIPAL1",
"hgnc_id": 27194,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.563+35190C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NR_125879.1",
"gene_symbol": "LOC101927157",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.479-9130C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Retinitis pigmentosa 49",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Retinitis pigmentosa 49",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}