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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: 17-4960296-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4960296&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4960296,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004890.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser",
"transcript": "NM_004890.3",
"protein_id": "NP_004881.2",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 227,
"cds_start": 265,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000206020.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004890.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser",
"transcript": "ENST00000206020.8",
"protein_id": "ENSP00000206020.3",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 227,
"cds_start": 265,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004890.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000206020.8"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.232G>A",
"hgvs_p": "p.Gly78Ser",
"transcript": "ENST00000575142.5",
"protein_id": "ENSP00000461145.1",
"transcript_support_level": 1,
"aa_start": 78,
"aa_end": null,
"aa_length": 194,
"cds_start": 232,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000575142.5"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser",
"transcript": "ENST00000859822.1",
"protein_id": "ENSP00000529881.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 226,
"cds_start": 265,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859822.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser",
"transcript": "ENST00000918591.1",
"protein_id": "ENSP00000588650.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 226,
"cds_start": 265,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918591.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser",
"transcript": "ENST00000949753.1",
"protein_id": "ENSP00000619812.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 226,
"cds_start": 265,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949753.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.259G>A",
"hgvs_p": "p.Gly87Ser",
"transcript": "ENST00000949752.1",
"protein_id": "ENSP00000619811.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 225,
"cds_start": 259,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949752.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.256G>A",
"hgvs_p": "p.Gly86Ser",
"transcript": "ENST00000918593.1",
"protein_id": "ENSP00000588652.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 224,
"cds_start": 256,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918593.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.112G>A",
"hgvs_p": "p.Gly38Ser",
"transcript": "ENST00000573366.5",
"protein_id": "ENSP00000458405.1",
"transcript_support_level": 3,
"aa_start": 38,
"aa_end": null,
"aa_length": 176,
"cds_start": 112,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000573366.5"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.174+163G>A",
"hgvs_p": null,
"transcript": "ENST00000918592.1",
"protein_id": "ENSP00000588651.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 176,
"cds_start": null,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918592.1"
},
{
"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": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.186G>A",
"hgvs_p": null,
"transcript": "ENST00000572148.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000572148.1"
},
{
"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": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.386G>A",
"hgvs_p": null,
"transcript": "ENST00000573805.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000573805.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.210-106G>A",
"hgvs_p": null,
"transcript": "ENST00000575784.2",
"protein_id": "ENSP00000458264.1",
"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": "ENST00000575784.2"
}
],
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"dbsnp": "rs772163068",
"frequency_reference_population": 6.8405535e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84055e-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": 0.8708833456039429,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.57,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9282,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.221,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004890.3",
"gene_symbol": "SPAG7",
"hgnc_id": 11216,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Gly89Ser"
}
],
"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
}