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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: 3-142449474-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142449474&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 142449474,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_001184.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7890A>G",
"hgvs_p": "p.Glu2630Glu",
"transcript": "NM_001184.4",
"protein_id": "NP_001175.2",
"transcript_support_level": null,
"aa_start": 2630,
"aa_end": null,
"aa_length": 2644,
"cds_start": 7890,
"cds_end": null,
"cds_length": 7935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000350721.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001184.4"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7890A>G",
"hgvs_p": "p.Glu2630Glu",
"transcript": "ENST00000350721.9",
"protein_id": "ENSP00000343741.4",
"transcript_support_level": 1,
"aa_start": 2630,
"aa_end": null,
"aa_length": 2644,
"cds_start": 7890,
"cds_end": null,
"cds_length": 7935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001184.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000350721.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.6599A>G",
"hgvs_p": null,
"transcript": "ENST00000513291.2",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000513291.2"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7737A>G",
"hgvs_p": "p.Glu2579Glu",
"transcript": "ENST00000936442.1",
"protein_id": "ENSP00000606501.1",
"transcript_support_level": null,
"aa_start": 2579,
"aa_end": null,
"aa_length": 2593,
"cds_start": 7737,
"cds_end": null,
"cds_length": 7782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936442.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7698A>G",
"hgvs_p": "p.Glu2566Glu",
"transcript": "NM_001354579.2",
"protein_id": "NP_001341508.1",
"transcript_support_level": null,
"aa_start": 2566,
"aa_end": null,
"aa_length": 2580,
"cds_start": 7698,
"cds_end": null,
"cds_length": 7743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354579.2"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7698A>G",
"hgvs_p": "p.Glu2566Glu",
"transcript": "ENST00000661310.1",
"protein_id": "ENSP00000499589.1",
"transcript_support_level": null,
"aa_start": 2566,
"aa_end": null,
"aa_length": 2580,
"cds_start": 7698,
"cds_end": null,
"cds_length": 7743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000661310.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7680A>G",
"hgvs_p": "p.Glu2560Glu",
"transcript": "ENST00000936443.1",
"protein_id": "ENSP00000606502.1",
"transcript_support_level": null,
"aa_start": 2560,
"aa_end": null,
"aa_length": 2574,
"cds_start": 7680,
"cds_end": null,
"cds_length": 7725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936443.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.990A>G",
"hgvs_p": "p.Glu330Glu",
"transcript": "ENST00000892891.1",
"protein_id": "ENSP00000562950.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 344,
"cds_start": 990,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892891.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7896A>G",
"hgvs_p": "p.Glu2632Glu",
"transcript": "XM_011512924.2",
"protein_id": "XP_011511226.1",
"transcript_support_level": null,
"aa_start": 2632,
"aa_end": null,
"aa_length": 2646,
"cds_start": 7896,
"cds_end": null,
"cds_length": 7941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512924.2"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.7704A>G",
"hgvs_p": "p.Glu2568Glu",
"transcript": "XM_011512925.2",
"protein_id": "XP_011511227.1",
"transcript_support_level": null,
"aa_start": 2568,
"aa_end": null,
"aa_length": 2582,
"cds_start": 7704,
"cds_end": null,
"cds_length": 7749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512925.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.*196A>G",
"hgvs_p": null,
"transcript": "ENST00000515810.1",
"protein_id": "ENSP00000421870.1",
"transcript_support_level": 3,
"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": "ENST00000515810.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.2748A>G",
"hgvs_p": null,
"transcript": "ENST00000653893.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000653893.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.2733A>G",
"hgvs_p": null,
"transcript": "ENST00000654170.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000654170.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.2976A>G",
"hgvs_p": null,
"transcript": "ENST00000656114.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000656114.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.*236A>G",
"hgvs_p": null,
"transcript": "ENST00000656590.1",
"protein_id": "ENSP00000499225.1",
"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": "ENST00000656590.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.3070A>G",
"hgvs_p": null,
"transcript": "ENST00000658083.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000658083.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.5430A>G",
"hgvs_p": null,
"transcript": "ENST00000665483.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000665483.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.4393A>G",
"hgvs_p": null,
"transcript": "ENST00000666447.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000666447.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.4622A>G",
"hgvs_p": null,
"transcript": "ENST00000666943.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000666943.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.*196A>G",
"hgvs_p": null,
"transcript": "ENST00000515810.1",
"protein_id": "ENSP00000421870.1",
"transcript_support_level": 3,
"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": "ENST00000515810.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.*236A>G",
"hgvs_p": null,
"transcript": "ENST00000656590.1",
"protein_id": "ENSP00000499225.1",
"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": "ENST00000656590.1"
},
{
"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": "ENSG00000295506",
"gene_hgnc_id": null,
"hgvs_c": "n.142+1192T>C",
"hgvs_p": null,
"transcript": "ENST00000730510.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000730510.1"
}
],
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"dbsnp": "rs750316781",
"frequency_reference_population": 6.844805e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8448e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5299999713897705,
"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": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.015,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001184.4",
"gene_symbol": "ATR",
"hgnc_id": 882,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.7890A>G",
"hgvs_p": "p.Glu2630Glu"
},
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000730510.1",
"gene_symbol": "ENSG00000295506",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+1192T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}