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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: 2-65313967-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=65313967&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 65313967,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_181784.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Tyr264Cys",
"transcript": "NM_181784.3",
"protein_id": "NP_861449.2",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 418,
"cds_start": 791,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000356388.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_181784.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Tyr264Cys",
"transcript": "ENST00000356388.9",
"protein_id": "ENSP00000348753.4",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 418,
"cds_start": 791,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_181784.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356388.9"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Tyr279Cys",
"transcript": "ENST00000452315.5",
"protein_id": "ENSP00000390595.1",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 431,
"cds_start": 836,
"cds_end": null,
"cds_length": 1298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452315.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.782A>G",
"hgvs_p": "p.Tyr261Cys",
"transcript": "NM_001128210.2",
"protein_id": "NP_001121682.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 415,
"cds_start": 782,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128210.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.782A>G",
"hgvs_p": "p.Tyr261Cys",
"transcript": "ENST00000443619.6",
"protein_id": "ENSP00000393697.2",
"transcript_support_level": 2,
"aa_start": 261,
"aa_end": null,
"aa_length": 415,
"cds_start": 782,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443619.6"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.557A>G",
"hgvs_p": "p.Tyr186Cys",
"transcript": "ENST00000931351.1",
"protein_id": "ENSP00000601410.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 340,
"cds_start": 557,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931351.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.437A>G",
"hgvs_p": "p.Tyr146Cys",
"transcript": "ENST00000421087.5",
"protein_id": "ENSP00000407627.1",
"transcript_support_level": 3,
"aa_start": 146,
"aa_end": null,
"aa_length": 232,
"cds_start": 437,
"cds_end": null,
"cds_length": 701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421087.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys",
"transcript": "XM_047443709.1",
"protein_id": "XP_047299665.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 398,
"cds_start": 731,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443709.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.422A>G",
"hgvs_p": "p.Tyr141Cys",
"transcript": "XM_017003576.2",
"protein_id": "XP_016859065.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 295,
"cds_start": 422,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003576.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.200A>G",
"hgvs_p": "p.Tyr67Cys",
"transcript": "XM_047443711.1",
"protein_id": "XP_047299667.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 221,
"cds_start": 200,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443711.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.588+2767A>G",
"hgvs_p": null,
"transcript": "XM_005264200.6",
"protein_id": "XP_005264257.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": null,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264200.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.579+2767A>G",
"hgvs_p": null,
"transcript": "XM_047443710.1",
"protein_id": "XP_047299666.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 245,
"cds_start": null,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443710.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.588+2767A>G",
"hgvs_p": null,
"transcript": "XM_005264202.6",
"protein_id": "XP_005264259.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": null,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264202.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "c.579+2767A>G",
"hgvs_p": null,
"transcript": "XM_047443712.1",
"protein_id": "XP_047299668.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": null,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443712.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "n.*624A>G",
"hgvs_p": null,
"transcript": "ENST00000426832.2",
"protein_id": "ENSP00000414551.2",
"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": "ENST00000426832.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"hgvs_c": "n.*624A>G",
"hgvs_p": null,
"transcript": "ENST00000426832.2",
"protein_id": "ENSP00000414551.2",
"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": "ENST00000426832.2"
}
],
"gene_symbol": "SPRED2",
"gene_hgnc_id": 17722,
"dbsnp": "rs142711233",
"frequency_reference_population": 0.000008681471,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000753202,
"gnomad_genomes_af": 0.0000197112,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8922853469848633,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.783,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7187,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.945,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_181784.3",
"gene_symbol": "SPRED2",
"hgnc_id": 17722,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Tyr264Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}